To whom it may concern,
We are working on a protein which has an N-linked glycosylation site.
We are having difficulty in getting X-plor to generate a proper .psf and .pdb
file for refinement when sugars are added to the input .pdb file. The following
contains the X-plor command input file used. The protein is separated into the
first 5 pdb files. File 2.pdb contains the Asn 65 which is N-linked to the first
sugar residue NAG (301). File 6.pdb and 7.pdb contain the sugar residues 301 and
302 respectively. Below the input file, we have included the message output generated
by X-plor. It seems to read all the input pdb files correctly, but when the patch,
B1N, is run to create the bond from the protein to the sugar, something goes wrong.
Similarly, the patch to create the glycosidic linkage goes awry too. The patches
are from the distributed toph3.cho and are unmodified. Just to prove that the atoms
are indeed in the pdb files we have included the 15 atom long sugar files 6.pdb
and 7.pdb( the 15 hydrogens are missing but we gather that that is not a problem )
along with the asn from 2.pdb at the bottom of this rather long post.
We appreciate any and all help in resolving this matter.
Thanks,
spacecby at u.washington.edu
{*-------------------------------------------------------------------------*}
Generate input file which doesn't work for sugars
{*-------------------------------------------------------------------------*}
topology @/sgi/local/xtal/xplor3.8/toppar/tophcsdx.pro
@/sgi/local/xtal/xplor3.8/toppar/toph3.cho end
parameter @/sgi/local/xtal/xplor3.8/toppar/protein_rep.param
@/sgi/local/xtal/xplor3.8/toppar/param3.cho end
{*-------------------------------------------------------------------------*}
segment {*Generate first bit.*}
name=" " {*This name has to match the *}
{*four characters in columns 73*}
{*through 76 in the coordinate *}
{*file; in XPLOR this name is *}
{*referred to as SEGId. *}
chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
coordinates @1.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
{*Sometimes different atom*}
vector do (name="O") ( name OT1 ) {*names are used. *}
vector do (name="OT") ( name OT2 )
vector do (name="CD1") ( name CD and resname ile )
coordinates @1.pdb {*Here we actually read the*}
{*coordinates. *}
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
segment {*Generate first bit.*}
name=" " {*This name has to match the *}
{*four characters in columns 73*}
{*through 76 in the coordinate *}
{*file; in XPLOR this name is *}
{*referred to as SEGId. *}
chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
coordinates @2.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
{*Sometimes different atom*}
vector do (name="O") ( name OT1 ) {*names are used. *}
vector do (name="OT") ( name OT2 )
vector do (name="CD1") ( name CD and resname ile )
coordinates @2.pdb {*Here we actually read the*}
{*coordinates. *}
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
segment {*Generate first bit.*}
name=" " {*This name has to match the *}
{*four characters in columns 73*}
{*through 76 in the coordinate *}
{*file; in XPLOR this name is *}
{*referred to as SEGId. *}
chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
coordinates @3.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
{*Sometimes different atom*}
vector do (name="O") ( name OT1 ) {*names are used. *}
vector do (name="OT") ( name OT2 )
vector do (name="CD1") ( name CD and resname ile )
coordinates @3.pdb {*Here we actually read the*}
{*coordinates. *}
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
segment {*Generate first bit.*}
name=" " {*This name has to match the *}
{*four characters in columns 73*}
{*through 76 in the coordinate *}
{*file; in XPLOR this name is *}
{*referred to as SEGId. *}
chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
coordinates @4.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
{*Sometimes different atom*}
vector do (name="O") ( name OT1 ) {*names are used. *}
vector do (name="OT") ( name OT2 )
vector do (name="CD1") ( name CD and resname ile )
coordinates @4.pdb {*Here we actually read the*}
{*coordinates. *}
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
segment {*Generate first bit.*}
name=" " {*This name has to match the *}
{*four characters in columns 73*}
{*through 76 in the coordinate *}
{*file; in XPLOR this name is *}
{*referred to as SEGId. *}
chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
coordinates @5.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
{*Sometimes different atom*}
vector do (name="O") ( name OT1 ) {*names are used. *}
vector do (name="OT") ( name OT2 )
vector do (name="CD1") ( name CD and resname ile )
coordinates @5.pdb {*Here we actually read the*}
{*coordinates. *}
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
segment {*Generate first bit.*}
name=" " {*This name has to match the *}
{*four characters in columns 73*}
{*through 76 in the coordinate *}
{*file; in XPLOR this name is *}
{*referred to as SEGId. *}
chain
coordinates @6.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
{*Sometimes different atom*}
vector do (name="O") ( name OT1 ) {*names are used. *}
vector do (name="OT") ( name OT2 )
vector do (name="CD1") ( name CD and resname ile )
coordinates @6.pdb {*Here we actually read the*}
{*coordinates. *}
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
segment {*Generate first bit.*}
name=" " {*This name has to match the *}
{*four characters in columns 73*}
{*through 76 in the coordinate *}
{*file; in XPLOR this name is *}
{*referred to as SEGId. *}
chain
coordinates @7.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
{*Sometimes different atom*}
vector do (name="O") ( name OT1 ) {*names are used. *}
vector do (name="OT") ( name OT2 )
vector do (name="CD1") ( name CD and resname ile )
coordinates @7.pdb {*Here we actually read the*}
{*coordinates. *}
{*-------------------------------------------------------------------------*}
{===>} {*Create S-S bridges.*}
patch disu
reference=1=( resid 76 )
reference=2=( resid 175 )
end
{===>} {*Create NAG ASN link.*}
patch B1N
reference=1=( resid 65 )
reference=2=(resid 301 )
end
patch B14 {*Create NAG NAG bond.*}
reference=1=( resid 301 )
reference=2=( resid 302 )
end
{===>} {set hydrogen flag: must be TRUE for NMR, atomic resolution X-ray }
{ crystallography or modelling. Set the FALSE for most X-ray }
{ crystallographic applications at resolution > 1. A }
evaluate ($hydrogen_flag=FALSE)
if ($hydrogen_flag=TRUE) then
flags exclude vdw elec end {*Do QUICK hydrogen building w/o*}
{*vdw and elec terms. *}
hbuild {*This statement builds *}
selection=( hydrogen ) {*missing hydrogens, which are*}
phistep=45 {*needed for the force field. *}
end
constraints fix=( not hydrogen ) end {* Minimize hydrogen positions. *}
flags include vdw end
minimize powell
nstep=40
end
constraints fix=( not all ) end
else
delete selection=( hydrogen ) end
end if
{* Set occupancies and b-factors if necessary *}
vector do (q=1.0 ) ( all )
vector do (b=15.) ( all )
write coordinates output=model12_gen.pdb end {*Write out coordinates.*}
write structure output=model12.psf end {*Write out structure file.*}
stop
{*-----------------------------------------------------------------------------*}
X-plor output messages
{*-----------------------------------------------------------------------------*}
X-PLOR> topology @/sgi/local/xtal/xplor3.8/toppar/tophcsdx.pro
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/tophcsdx.pro opened.
RTFRDR>remarks file TOPPAR/tophcsdx_new.pro (5/26/92)
RTFRDR>REMARKS TOPHCSDx.PRO: Original XPLOR toph19x.pro modified according to
RTFRDR>REMARKS R. A. Engh and R. Huber, Acta Cryst, Sect A, 1991)
RTFRDR>REMARKS with additional atom types.
RTFRDR>REMARKS ===============================
RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs.
RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations.
RTFRDR>REMARKS Amide charges set to match the experimental dipole moment.
RTFRDR>REMARKS Default for HIStidines is the doubly protonated state
RTFRDR>
RTFRDR>!
RTFRDR>! Please cite the following reference when using these parameters:
RTFRDR>! Engh, R.A. and Huber, R. (1991). Accurate Bond and
RTFRDR>! Angle Parameters for X-ray Protein-Structure Refinement,
RTFRDR>! Acta Cryst. A47, 392-400.
RTFRDR>!
RTFRDR>!
RTFRDR>
RTFRDR>set echo=false end
RTFRDR>set echo=true end
RTFRDR>
RTFRDR> @/sgi/local/xtal/xplor3.8/toppar/toph3.cho end
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph3.cho opened.
RTFRDR>REMARKS toph3.cho {pyranose sugar toplogy for refinement}
RTFRDR>REMARKS FOR USE WITH PARAM3.CHO AND CSD PROTEIN PARAMETERS
RTFRDR>REMARKS =====================================================
RTFRDR>REMARKS Bill Weis 10-July-1988
RTFRDR>REMARKS Also see PARAM1.CHO for parameters.
RTFRDR>REMARKS Charges taken from John Brady's glucose topology file for ring,
RTFRDR>REMARKS others from protein parameter file.
RTFRDR>REMARKS Idealized values for impropers at ring carbons to allow simple
RTFRDR>REMARKS construction of various anomers/epimers.
RTFRDR>REMARKS Any other hexose or link can be easily constructed by analogy to these.
RTFRDR>
RTFRDR>REMARKS Additions 6-March-1992 Bill Weis for use with PARAM2.CHO
RTFRDR>REMARKS New atom types CCA, CCE, OA for the C1 & O1 positions to account
RTFRDR>REMARKS for different bond and angle values due to the anomeric effect.
RTFRDR>REMARKS More accurate equilibrium values for bond angle around this oxygen
RTFRDR>REMARKS in glycosidic linkages. CCE for equatorial O1, CCA for
RTFRDR>REMAKRS axial O1. For free sugar, keep OH1 as O1 atomtype; changed to OA
RTFRDR>REMARKS for linkages.
RTFRDR>REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103;
RTFRDR>REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879.
RTFRDR>
RTFRDR>REMARKS Additional CC6 atomtype for exocyclic carbon 5/11/92
RTFRDR>
RTFRDR>set echo=false end
RTFRDR>
RTFRDR> end
X-PLOR>
X-PLOR>parameter @/sgi/local/xtal/xplor3.8/toppar/protein_rep.param
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/protein_rep.param opened.
PARRDR>remarks file toppar/protein_rep.param
PARRDR>remarks Parameter file including bond and angle parameters
PARRDR>remarks derived from Cambridge Data Base model structures
PARRDR>remarks (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991).
PARRDR>remarks Nonbonded parameters taken from PROLSQ using REPEL function.
PARRDR>remarks Small dihedral angle energy constants set to zero. All other
PARRDR>remarks dihedral and improper energy constants set to uniform values.
PARRDR>remarks Water parameters are included.
PARRDR>
PARRDR>!
PARRDR>! References:
PARRDR>! Engh, R.A. and Huber, R. (1991). Accurate Bond and
PARRDR>! Angle Parameters for X-ray Protein-Structure Refinement,
PARRDR>! Acta Cryst. A47, 392-400.
PARRDR>!
PARRDR>! Hendrickson W.A. and Konnert J.H. in "Computing in
PARRDR>! Crystallography" (ed. R. Diamond, S. Ramaseshan
PARRDR>! and K. Venkatesan) (Bangalore, Indian Institute of
PARRDR>! Science, 1980) 13.01-13.23
PARRDR>!
PARRDR>
PARRDR>
PARRDR>
PARRDR>set echo=off message=off end
PARRDR> @/sgi/local/xtal/xplor3.8/toppar/param3.cho end
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/param3.cho opened.
PARRDR>
PARRDR>REMARKS Parameter file for pyranose sugars
PARRDR>REMARKS ==================================
PARRDR>REMARKS Bill Weis 10-July-1988
PARRDR>REMARKS Additions for atom type combinations not covered in PARAM19X.PRO.
PARRDR>REMARKS Needed additions are for ether oxygen and aliphatic carbon in all-atom
PARRDR>REMARKS representation used for sugars (type CC). Ditto for type HA.
PARRDR>REMARKS Values from J. Brady glucose parameters unless noted.
PARRDR>REMARKS These should be sufficient for refinement.
PARRDR>
PARRDR>REMARKS Additions 6-March-1992 Bill Weis
PARRDR>REMARKS New atom types CCA, CCE, OA for the C1 & O1 positions to account
PARRDR>REMARKS for different bond and angle values due to the anomeric effect.
PARRDR>REMARKS More accurate equilibrium values for bond angle around this oxygen
PARRDR>REMARKS in glycosidic linkages. CCE for equatorial O1, CCA for
PARRDR>REMAKRS axial O1. For free sugar, keep OH1 as O1 atomtype; changed to OA
PARRDR>REMARKS for linkages.
PARRDR>REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103;
PARRDR>REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879.
PARRDR>
PARRDR>REMARKS This set has been modified to be roughly consistent with
PARRDR>REMARKS the csd-derived protein parameters of Engh and Huber. For use
PARRDR>REMARKS with PARAMCSDX_MOD.PRO. New atom type CC6 for exocyclic 6 carbon
PARRDR>REMARKS Bill Weis 5/11/92
PARRDR>
PARRDR>set echo=false end
PARRDR>
PARRDR> end
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>
X-PLOR> segment {*Generate first bit.*}
SEGMENT>
SEGMENT> name=" " {*This name has to match the *}
SEGMENT> {*four characters in columns 73*}
SEGMENT> {*through 76 in the coordinate *}
SEGMENT> {*file; in XPLOR this name is *}
SEGMENT> {*referred to as SEGId. *}
SEGMENT>
SEGMENT> chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence
CHAIN>SET ECHO=FALSE END
CHAIN>
CHAIN> coordinates @1.pdb {*interpret coordinate file to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file 1.pdb opened.
COOR>ATOM 1 N ILE 8 49.186 33.900 14.272 1.00 15.00
MAPIC: Atom numbers being modified
MAPIC: Atom numbers being modified
CHAIN> {*interpret coordinate file to*}
CHAIN> end {*obtain the sequence. *}
SEGMENT> end
SEGMNT: 32 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 270(MAXA= 36000) NBOND= 277(MAXB= 36000)
NTHETA= 404(MAXT= 50000) NGRP= 34(MAXGRP= 36000)
NPHI= 159(MAXP= 60000) NIMPHI= 135(MAXIMP= 24000)
NDON= 44(MAXPAD= 10000) NACC= 41(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> {*Sometimes different atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used. *}
SELRPN: 1 atoms have been selected out of 270
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 1 atoms have been selected out of 270
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 1 atoms have been selected out of 270
X-PLOR>
X-PLOR> coordinates @1.pdb {*Here we actually read the*}
ASSFIL: file 1.pdb opened.
COOR>ATOM 1 N ILE 8 49.186 33.900 14.272 1.00 15.00
COOR>ATOM 2 CD1 ILE 8 50.755 35.272 17.630 1.00 15.00
%READC-ERR: still 43 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates. *}
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>
X-PLOR> segment {*Generate first bit.*}
SEGMENT>
SEGMENT> name=" " {*This name has to match the *}
SEGMENT> {*four characters in columns 73*}
SEGMENT> {*through 76 in the coordinate *}
SEGMENT> {*file; in XPLOR this name is *}
SEGMENT> {*referred to as SEGId. *}
SEGMENT>
SEGMENT> chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence
CHAIN>SET ECHO=FALSE END
CHAIN>
CHAIN> coordinates @2.pdb {*interpret coordinate file to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file 2.pdb opened.
COOR>ATOM 228 N ILE 41 43.788 31.593 22.173 1.00 15.00
MAPIC: Atom numbers being modified
MAPIC: Atom numbers being modified
CHAIN> {*interpret coordinate file to*}
CHAIN> end {*obtain the sequence. *}
SEGMENT> end
SEGMNT: 32 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 549(MAXA= 36000) NBOND= 560(MAXB= 36000)
NTHETA= 814(MAXT= 50000) NGRP= 68(MAXGRP= 36000)
NPHI= 312(MAXP= 60000) NIMPHI= 273(MAXIMP= 24000)
NDON= 93(MAXPAD= 10000) NACC= 86(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> {*Sometimes different atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used. *}
SELRPN: 1 atoms have been selected out of 549
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 1 atoms have been selected out of 549
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 1 atoms have been selected out of 549
X-PLOR>
X-PLOR> coordinates @2.pdb {*Here we actually read the*}
ASSFIL: file 2.pdb opened.
COOR>ATOM 228 N ILE 41 43.788 31.593 22.173 1.00 15.00
COOR>ATOM 229 CD1 ILE 41 39.529 31.928 24.351 1.00 15.00
%READC-ERR: still 92 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates. *}
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>
X-PLOR> segment {*Generate first bit.*}
SEGMENT>
SEGMENT> name=" " {*This name has to match the *}
SEGMENT> {*four characters in columns 73*}
SEGMENT> {*through 76 in the coordinate *}
SEGMENT> {*file; in XPLOR this name is *}
SEGMENT> {*referred to as SEGId. *}
SEGMENT>
SEGMENT> chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence
CHAIN>SET ECHO=FALSE END
CHAIN>
CHAIN> coordinates @3.pdb {*interpret coordinate file to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file 3.pdb opened.
COOR>ATOM 457 CB ALA 74 43.158 16.211 37.281 1.00 15.00
MAPIC: Atom numbers being modified
MAPIC: Atom numbers being modified
CHAIN> {*interpret coordinate file to*}
CHAIN> end {*obtain the sequence. *}
SEGMENT> end
SEGMNT: 24 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 736(MAXA= 36000) NBOND= 751(MAXB= 36000)
NTHETA= 1091(MAXT= 50000) NGRP= 94(MAXGRP= 36000)
NPHI= 414(MAXP= 60000) NIMPHI= 370(MAXIMP= 24000)
NDON= 122(MAXPAD= 10000) NACC= 119(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> {*Sometimes different atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used. *}
SELRPN: 1 atoms have been selected out of 736
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 1 atoms have been selected out of 736
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 0 atoms have been selected out of 736
X-PLOR>
X-PLOR> coordinates @3.pdb {*Here we actually read the*}
ASSFIL: file 3.pdb opened.
COOR>ATOM 457 CB ALA 74 43.158 16.211 37.281 1.00 15.00
COOR>ATOM 458 C ALA 74 43.390 18.122 38.901 1.00 15.00
%READC-ERR: still 121 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates. *}
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>
X-PLOR> segment {*Generate first bit.*}
SEGMENT>
SEGMENT> name=" " {*This name has to match the *}
SEGMENT> {*four characters in columns 73*}
SEGMENT> {*through 76 in the coordinate *}
SEGMENT> {*file; in XPLOR this name is *}
SEGMENT> {*referred to as SEGId. *}
SEGMENT>
SEGMENT> chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence
CHAIN>SET ECHO=FALSE END
CHAIN>
CHAIN> coordinates @4.pdb {*interpret coordinate file to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file 4.pdb opened.
COOR>ATOM 615 CB ALA 100 58.051 37.875 28.748 1.00 15.00
MAPIC: Atom numbers being modified
MAPIC: Atom numbers being modified
CHAIN> {*interpret coordinate file to*}
CHAIN> end {*obtain the sequence. *}
SEGMENT> end
SEGMNT: 7 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 781(MAXA= 36000) NBOND= 795(MAXB= 36000)
NTHETA= 1157(MAXT= 50000) NGRP= 103(MAXGRP= 36000)
NPHI= 436(MAXP= 60000) NIMPHI= 390(MAXIMP= 24000)
NDON= 131(MAXPAD= 10000) NACC= 127(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> {*Sometimes different atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used. *}
SELRPN: 1 atoms have been selected out of 781
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 1 atoms have been selected out of 781
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 0 atoms have been selected out of 781
X-PLOR>
X-PLOR> coordinates @4.pdb {*Here we actually read the*}
ASSFIL: file 4.pdb opened.
COOR>ATOM 615 CB ALA 100 58.051 37.875 28.748 1.00 15.00
COOR>ATOM 616 C ALA 100 59.426 39.396 27.289 1.00 15.00
%READC-ERR: still 130 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates. *}
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR> segment {*Generate first bit.*}
SEGMENT>
SEGMENT> name=" " {*This name has to match the *}
SEGMENT> {*four characters in columns 73*}
SEGMENT> {*through 76 in the coordinate *}
SEGMENT> {*file; in XPLOR this name is *}
SEGMENT> {*referred to as SEGId. *}
SEGMENT>
SEGMENT> chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep
ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence
CHAIN>SET ECHO=FALSE END
CHAIN>
CHAIN> coordinates @5.pdb {*interpret coordinate file to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file 5.pdb opened.
COOR>ATOM 651 CB ALA 111 37.082 48.685 28.204 1.00 15.00
MAPIC: Atom numbers being modified
MAPIC: Atom numbers being modified
CHAIN> {*interpret coordinate file to*}
CHAIN> end {*obtain the sequence. *}
SEGMENT> end
SEGMNT: 67 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1371(MAXA= 36000) NBOND= 1398(MAXB= 36000)
NTHETA= 2030(MAXT= 50000) NGRP= 172(MAXGRP= 36000)
NPHI= 766(MAXP= 60000) NIMPHI= 689(MAXIMP= 24000)
NDON= 240(MAXPAD= 10000) NACC= 206(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> {*Sometimes different atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used. *}
SELRPN: 1 atoms have been selected out of 1371
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 1 atoms have been selected out of 1371
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 4 atoms have been selected out of 1371
X-PLOR>
X-PLOR> coordinates @5.pdb {*Here we actually read the*}
ASSFIL: file 5.pdb opened.
COOR>ATOM 651 CB ALA 111 37.082 48.685 28.204 1.00 15.00
COOR>ATOM 652 C ALA 111 37.246 47.359 30.216 1.00 15.00
%READC-ERR: still 239 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates. *}
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR> segment {*Generate first bit.*}
SEGMENT>
SEGMENT> name=" " {*This name has to match the *}
SEGMENT> {*four characters in columns 73*}
SEGMENT> {*through 76 in the coordinate *}
SEGMENT> {*file; in XPLOR this name is *}
SEGMENT> {*referred to as SEGId. *}
SEGMENT>
SEGMENT> chain
CHAIN>
CHAIN> coordinates @6.pdb {*interpret coordinate file to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file 6.pdb opened.
COOR>ATOM 1132 C1 NAG 301 51.140 33.159 50.368 1.00 15.00
CHAIN> {*interpret coordinate file to*}
CHAIN> end {*obtain the sequence. *}
SEGMENT> end
SEGMNT: 1 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1401(MAXA= 36000) NBOND= 1428(MAXB= 36000)
NTHETA= 2083(MAXT= 50000) NGRP= 173(MAXGRP= 36000)
NPHI= 780(MAXP= 60000) NIMPHI= 696(MAXIMP= 24000)
NDON= 245(MAXPAD= 10000) NACC= 212(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> {*Sometimes different atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used. *}
SELRPN: 0 atoms have been selected out of 1401
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 0 atoms have been selected out of 1401
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 0 atoms have been selected out of 1401
X-PLOR>
X-PLOR> coordinates @6.pdb {*Here we actually read the*}
ASSFIL: file 6.pdb opened.
COOR>ATOM 1132 C1 NAG 301 51.140 33.159 50.368 1.00 15.00
COOR>ATOM 1133 C2 NAG 301 50.914 31.796 49.679 1.00 15.00
%READC-ERR: still 254 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates. *}
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR> segment {*Generate first bit.*}
SEGMENT>
SEGMENT> name=" " {*This name has to match the *}
SEGMENT> {*four characters in columns 73*}
SEGMENT> {*through 76 in the coordinate *}
SEGMENT> {*file; in XPLOR this name is *}
SEGMENT> {*referred to as SEGId. *}
SEGMENT>
SEGMENT> chain
CHAIN>
CHAIN> coordinates @7.pdb {*interpret coordinate file to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file 7.pdb opened.
COOR>ATOM 1146 C1 NAG 302 50.629 38.155 47.096 1.00 15.00
CHAIN> {*interpret coordinate file to*}
CHAIN> end {*obtain the sequence. *}
SEGMENT> end
SEGMNT: 1 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1431(MAXA= 36000) NBOND= 1458(MAXB= 36000)
NTHETA= 2136(MAXT= 50000) NGRP= 174(MAXGRP= 36000)
NPHI= 794(MAXP= 60000) NIMPHI= 703(MAXIMP= 24000)
NDON= 250(MAXPAD= 10000) NACC= 218(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> {*Sometimes different atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used. *}
SELRPN: 0 atoms have been selected out of 1431
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 0 atoms have been selected out of 1431
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 0 atoms have been selected out of 1431
X-PLOR>
X-PLOR> coordinates @7.pdb {*Here we actually read the*}
ASSFIL: file 7.pdb opened.
COOR>ATOM 1146 C1 NAG 302 50.629 38.155 47.096 1.00 15.00
COOR>ATOM 1147 C2 NAG 302 50.947 38.411 48.585 1.00 15.00
%READC-ERR: still 269 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates. *}
X-PLOR>
X-PLOR>{*-------------------------------------------------------------------------*}
X-PLOR>
X-PLOR>{===>} {*Create S-S bridges.*}
X-PLOR> patch disu
PATCH> reference=1=( resid 76 )
SELRPN: 7 atoms have been selected out of 1431
PATCH> reference=2=( resid 175 )
SELRPN: 7 atoms have been selected out of 1431
PATCH> end
MAPIC: Atom numbers being modified
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1431(MAXA= 36000) NBOND= 1459(MAXB= 36000)
NTHETA= 2138(MAXT= 50000) NGRP= 176(MAXGRP= 36000)
NPHI= 797(MAXP= 60000) NIMPHI= 703(MAXIMP= 24000)
NDON= 250(MAXPAD= 10000) NACC= 218(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR>{===>} {*Create NAG ASN link.*}
X-PLOR> patch B1N
PATCH> reference=1=( resid 65 )
SELRPN: 11 atoms have been selected out of 1431
PATCH> reference=2=(resid 301 )
SELRPN: 30 atoms have been selected out of 1431
PATCH> end
%PATCH-ERR: atom +ND2 not found
%PATCH-ERR: atom +HD22 not found
%PATCH-ERR: atom +HD21 not found
%PATCH-ERR: atom -C1 not found
%PATCH-ERR: atom -O1 not found
%PATCH-ERR: atom -HO1 not found
%PATCH-ERR: bond -C1 +ND2 not found
%PATCH-ERR: angle +CG +ND2 -C1 not found
%PATCH-ERR: angle +HD22 +ND2 -C1 not found
%PATCH-ERR: angle +ND2 -C1 -C2 not found
%PATCH-ERR: angle +ND2 -C1 -O5 not found
%PATCH-ERR: angle +ND2 -C1 -H1 not found
%PATCH-ERR: dihedral +CG +ND2 -C1 -H1 not found
%PATCH-ERR: improper +ND2 -C1 +HD22 +CG not found
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1431(MAXA= 36000) NBOND= 1459(MAXB= 36000)
NTHETA= 2138(MAXT= 50000) NGRP= 176(MAXGRP= 36000)
NPHI= 797(MAXP= 60000) NIMPHI= 703(MAXIMP= 24000)
NDON= 250(MAXPAD= 10000) NACC= 218(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> patch B14 {*Create NAG NAG bond.*}
PATCH> reference=1=( resid 301 )
SELRPN: 30 atoms have been selected out of 1431
PATCH> reference=2=( resid 302 )
SELRPN: 30 atoms have been selected out of 1431
PATCH> end
%PATCH-ERR: atom +O4 not found
%PATCH-ERR: atom +C4 not found
%PATCH-ERR: atom +HO4 not found
%PATCH-ERR: atom -C1 not found
%PATCH-ERR: atom -O1 not found
%PATCH-ERR: atom -HO1 not found
%PATCH-ERR: bond -C1 +O4 not found
%PATCH-ERR: angle +C4 +O4 -C1 not found
%PATCH-ERR: angle +O4 -C1 -H1 not found
%PATCH-ERR: angle +O4 -C1 -O5 not found
%PATCH-ERR: angle +O4 -C1 -C2 not found
%PATCH-ERR: dihedral +C4 +O4 -C1 -H1 not found
%PATCH-ERR: dihedral +C4 +O4 -C1 -O5 not found
%PATCH-ERR: dihedral +C4 +O4 -C1 -C2 not found
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1431(MAXA= 36000) NBOND= 1459(MAXB= 36000)
NTHETA= 2138(MAXT= 50000) NGRP= 176(MAXGRP= 36000)
NPHI= 797(MAXP= 60000) NIMPHI= 703(MAXIMP= 24000)
NDON= 250(MAXPAD= 10000) NACC= 218(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR>{===>} {set hydrogen flag: must be TRUE for NMR, atomic resolution X-ray }
X-PLOR> { crystallography or modelling. Set the FALSE for most X-ray }
X-PLOR> { crystallographic applications at resolution > 1. A }
X-PLOR> evaluate ($hydrogen_flag=FALSE)
EVALUATE: symbol $HYDROGEN_FLAG set to FALSE (logical)
X-PLOR>
X-PLOR> if ($hydrogen_flag=TRUE) then
NEXTCD: condition evaluated as false
X-PLOR> flags exclude vdw elec end {*Do QUICK hydrogen building w/o*}
X-PLOR> {*vdw and elec terms. *}
X-PLOR> hbuild {*This statement builds *}
X-PLOR> selection=( hydrogen ) {*missing hydrogens, which are*}
X-PLOR> phistep=45 {*needed for the force field. *}
X-PLOR> end
X-PLOR>
X-PLOR> constraints fix=( not hydrogen ) end {* Minimize hydrogen positions. *}
X-PLOR> flags include vdw end
X-PLOR> minimize powell
X-PLOR> nstep=40
X-PLOR> end
X-PLOR> constraints fix=( not all ) end
X-PLOR> else
X-PLOR> delete selection=( hydrogen ) end
SELRPN: 270 atoms have been selected out of 1431
MAPIC: Atom numbers being modified
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 1161(MAXA= 36000) NBOND= 1189(MAXB= 36000)
NTHETA= 1627(MAXT= 50000) NGRP= 176(MAXGRP= 36000)
NPHI= 707(MAXP= 60000) NIMPHI= 535(MAXIMP= 24000)
NDON= 0(MAXPAD= 10000) NACC= 218(MAXPAD= 10000)
NNB= 0(MAXNB= 4000)
X-PLOR> end if
X-PLOR>
X-PLOR> {* Set occupancies and b-factors if necessary *}
X-PLOR> vector do (q=1.0 ) ( all )
SELRPN: 1161 atoms have been selected out of 1161
X-PLOR> vector do (b=15.) ( all )
SELRPN: 1161 atoms have been selected out of 1161
X-PLOR>
X-PLOR> write coordinates output=model12_gen.pdb end {*Write out coordinates.*}
ASSFIL: file model12_gen.pdb opened.
X-PLOR> write structure output=model12.psf end {*Write out structure file.*}
ASSFIL: file model12.psf opened.
X-PLOR> stop
CSTACK: size= 40000 used= 2912 current= 0
HEAP: maximum use= 71493 current use= 0
X-PLOR: total CPU time= 2.5009 s
X-PLOR: entry time at 19:50:06 30-Apr-98
X-PLOR: exit time at 19:50:14 30-Apr-98
{*-----------------------------------------------------------------------------------*}
input pdb files
{*-----------------------------------------------------------------------------------*}
{*---------------------------------------------*}
Excerpt from 2.pdb
{*---------------------------------------------*}
ATOM 403 N ASN 65 48.464 42.545 42.942 1.00 15.00
ATOM 404 ND2 ASN 65 50.062 38.786 45.595 1.00 15.00
ATOM 405 OD1 ASN 65 50.951 39.678 43.765 1.00 15.00
ATOM 406 CG ASN 65 50.133 39.733 44.687 1.00 15.00
ATOM 407 CB ASN 65 49.155 40.925 44.729 1.00 15.00
ATOM 408 CA ASN 65 48.520 41.195 43.410 1.00 15.00
ATOM 409 C ASN 65 47.505 40.223 42.913 1.00 15.00
ATOM 410 O ASN 65 46.788 39.591 43.733 1.00 15.00
{*---------------------------------------------*}
sugar input files 6 and 7.pdb
{*---------------------------------------------*}
ATOM 1132 C1 NAG 301 51.140 33.159 50.368 1.00 15.00
ATOM 1133 C2 NAG 301 50.914 31.796 49.679 1.00 15.00
ATOM 1134 C3 NAG 301 50.457 30.700 50.646 1.00 15.00
ATOM 1135 C4 NAG 301 51.377 30.689 51.857 1.00 15.00
ATOM 1136 C5 NAG 301 51.365 32.058 52.555 1.00 15.00
ATOM 1137 C6 NAG 301 52.218 32.182 53.834 1.00 15.00
ATOM 1138 C7 NAG 301 50.067 31.460 47.387 1.00 15.00
ATOM 1139 C8 NAG 301 48.981 31.633 46.334 1.00 15.00
ATOM 1140 N2 NAG 301 49.894 31.935 48.632 1.00 15.00
ATOM 1141 O3 NAG 301 50.594 29.477 49.901 1.00 15.00
ATOM 1142 O4 NAG 301 50.918 29.699 52.763 1.00 15.00
ATOM 1143 O5 NAG 301 51.846 33.024 51.609 1.00 15.00
ATOM 1144 O6 NAG 301 53.586 32.061 53.490 1.00 15.00
ATOM 1145 O7 NAG 301 51.106 30.858 47.092 1.00 15.00
ATOM 1146 O1 NAG 301 50.062 38.786 45.595 1.00 15.00
END
ATOM 1146 C1 NAG 302 50.629 38.155 47.096 1.00 15.00
ATOM 1147 C2 NAG 302 50.947 38.411 48.585 1.00 15.00
ATOM 1148 C3 NAG 302 51.507 37.179 49.303 1.00 15.00
ATOM 1149 C4 NAG 302 50.613 35.983 49.009 1.00 15.00
ATOM 1150 C5 NAG 302 50.532 35.731 47.495 1.00 15.00
ATOM 1151 C6 NAG 302 49.697 34.513 47.049 1.00 15.00
ATOM 1152 C7 NAG 302 51.581 40.787 48.776 1.00 15.00
ATOM 1153 C8 NAG 302 52.642 41.873 48.889 1.00 15.00
ATOM 1154 N2 NAG 302 51.934 39.493 48.701 1.00 15.00
ATOM 1155 O3 NAG 302 51.451 37.515 50.700 1.00 15.00
ATOM 1156 O4 NAG 302 51.166 34.841 49.644 1.00 15.00
ATOM 1157 O5 NAG 302 49.960 36.902 46.896 1.00 15.00
ATOM 1158 O6 NAG 302 48.336 34.748 47.361 1.00 15.00
ATOM 1159 O7 NAG 302 50.386 41.105 48.774 1.00 15.00
ATOM 1160 O1 NAG 302 50.918 29.699 52.763 1.00 15.00
END
