hi,
i have a problem when trying to run HBUILD in xplor on my sgi.
basically, it gives me a core dump and i don't know how to trace
down the problem. i don't believe it's a problem of running out
of swap space, i don't get a message indicating that, and if i
reduce my protein to only 5 amino acids, i still crash with a
core dump. just in case, i tried increasing swap space, and it
had no affect. i get the same problem when i use the sample
'generate.inp' file provided in the tutorial directory of the
xplor distribution. if i comment out the HBUILD commands in the
input file, the program runs without a problem, and everything looks
normal - except that the output coordinate file has xyz coordinates
of 9999.000, which is to be expected without a HBUILD.
some specifics: i'm running xplor on an SGI Indigo2 XZ, with a
R4400 processor, with 64 MB memory and 2GB disk. i'm running IRIX
version 5.2. I'm using XPLOR version 3.1
i'm including an output .log file i obtained when running the above
mentioned 'generate.inp' provided with the distribution tape.
if anyone has had a similar problem, or even can suggest possible
solutions - i would be most beholding.
thanks,
marilyn yoder
myoder at cctr.umkc.edu
----------------------------start of generate.log ----------------
X-PLOR: V3.1f user: myoder on: sgi at: 01-Aug-95 13:39:24
Author: Axel T. Brunger
Copyright: 1988-92 (Yale University), 1987 (Harvard University)
X-PLOR> remarks file generate/generate.inp
X-PLOR> remarks Generate structure file and hydrogens for a protein
X-PLOR>
X-PLOR> topology @/usr/local/apps/xplor/toppar/tophcsdx.pro end
{*Read topology file.*}
ASSFIL: file /usr/local/apps/xplor/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>set echo=false end
RTFRDR>set echo=true end
RTFRDR>
RTFRDR> end {*Read topology file.*}
X-PLOR>
X-PLOR> parameter
PARRDR>
PARRDR>@/usr/local/apps/xplor/toppar/parhcsdx.pro
{*Read empirical potential*}
ASSFIL: file /usr/local/apps/xplor/toppar/parhcsdx.pro opened.
PARRDR>REMARK Parameter file including bond and angle parameters
PARRDR>REMARK derived from Cambridge Data Base model structures
PARRDR>REMARK (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991).
PARRDR>REMARK Dihedral, improper, and non-bonded parameters taken
PARRDR>REMARK from param19x (XPLOR--Axel T. Brunger, Yale University,
PARRDR>REMARK BRUNGER at YALEVMS) and assigned to new atom types
PARRDR>REMARK where appropriate.
PARRDR>
PARRDR>set echo=false end
PARRDR> {*Read empirical potential*}
PARRDR> {*parameter file
CHARMM19 *}
PARRDR> {*with modifications.
*}
PARRDR>
PARRDR> nbonds {*This statement specifies
the *}
NBDSET> atom cdie shift eps=1.0 e14fac=0.4 {*nonbonded interaction
energy *}
NBDSET> cutnb=7.5 ctonnb=6.0 ctofnb=6.5 {*options. Note the reduced
*}
NBDSET> nbxmod=5 vswitch {*nonbonding cutoff to save
some*}
NBDSET> end {*CPU time. This statement
*}
PARRDR> {*overwrites the defaults in
*}
PARRDR> {*the parameter file.
*}
PARRDR> end
X-PLOR>
X-PLOR> segment {*Generate
protein.*}
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> chain
CHAIN> @/usr/local/apps/xplor/toppar/toph19.pep
{*Read peptide bond file; *}
ASSFIL: file /usr/local/apps/xplor/toppar/toph19.pep opened.
CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence
CHAIN>SET ECHO=FALSE END
CHAIN> {*Read peptide bond file; *}
CHAIN> coordinates @amy.pdb {*interpret coordinate file
to*}
SEGMNT: sequence read from coordinate file
ASSFIL: file amy.pdb opened.
COOR>ATOM 1 N ASP 1 5.493 42.415 10.706 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: 74 residues were inserted into segment " "
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 681(MAXA= 16000) NBOND= 693(MAXB= 16000)
NTHETA= 998(MAXT= 24000) NGRP= 76(MAXGRP= 16000)
NPHI= 384(MAXP= 30000) NIMPHI= 336(MAXIMP= 8000)
NDON= 123(MAXPAD= 4000) NACC= 116(MAXPAD= 4000)
NNB= 0(MAXNB= 3000)
X-PLOR> {*Sometimes different
atom*}
X-PLOR> vector do (name="O") ( name OT1 ) {*names are used.
*}
SELRPN: 1 atoms have been selected out of 681
X-PLOR> vector do (name="OT") ( name OT2 )
SELRPN: 1 atoms have been selected out of 681
X-PLOR> vector do (name="CD1") ( name CD and resname ile )
SELRPN: 2 atoms have been selected out of 681
X-PLOR>
X-PLOR> coordinates @amy.pdb {*Here we actually read
the*}
ASSFIL: file amy.pdb opened.
COOR>ATOM 1 N ASP 1 5.493 42.415 10.706 1.00 15.00
COOR>ATOM 2 OD2 ASP 1 6.077 41.076 14.572 1.00 15.00
%READC-ERR: still 123 missing coordinates (in selected subset)
X-PLOR> {*Here we actually read the*}
X-PLOR> {*coordinates.
*}
X-PLOR>
X-PLOR> {*The generation of
cofactors, *}
X-PLOR> {*waters, etc. would follow
here.*}
X-PLOR> {*Note that one has to
split*}
X-PLOR> {*the coordinate file
into *}
X-PLOR> {*separate files
containing *}
X-PLOR> {*the protein,
cofactors, *}
X-PLOR> {*substrate, water, etc.
*}
X-PLOR>
X-PLOR> {*Create a S-S
bridge.*}
X-PLOR> patch disu
PATCH> reference=1=( resid 11 )
SELRPN: 7 atoms have been selected out of 681
PATCH> reference=2=( resid 27 )
SELRPN: 7 atoms have been selected out of 681
PATCH> end
MAPIC: Atom numbers being modified
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 681(MAXA= 16000) NBOND= 694(MAXB= 16000)
NTHETA= 1000(MAXT= 24000) NGRP= 78(MAXGRP= 16000)
NPHI= 387(MAXP= 30000) NIMPHI= 336(MAXIMP= 8000)
NDON= 123(MAXPAD= 4000) NACC= 116(MAXPAD= 4000)
NNB= 0(MAXNB= 3000)
X-PLOR> patch disu
PATCH> reference=1=( resid 45 )
SELRPN: 7 atoms have been selected out of 681
PATCH> reference=2=( resid 73 )
SELRPN: 7 atoms have been selected out of 681
PATCH> end
MAPIC: Atom numbers being modified
XPLOR: current counts (number in parenthesis is maximum)
NATOM= 681(MAXA= 16000) NBOND= 695(MAXB= 16000)
NTHETA= 1002(MAXT= 24000) NGRP= 80(MAXGRP= 16000)
NPHI= 390(MAXP= 30000) NIMPHI= 336(MAXIMP= 8000)
NDON= 123(MAXPAD= 4000) NACC= 116(MAXPAD= 4000)
NNB= 0(MAXNB= 3000)
X-PLOR>
X-PLOR> flags exclude vdw elec end {*Do QUICK hydrogen building
w/o*}
X-PLOR> {*vdw and elec terms.
*}
X-PLOR>
X-PLOR> hbuild {*This statement builds
*}
HBUILD> selection=( hydrogen ) {*missing hydrogens, which
are*}
SELRPN: 123 atoms have been selected out of 681
HBUILD> phistep=4 {*needed for the force
field. *}
HBUILD> end
HBUILD: dihedral PHI STePs for spin = 4.0000
HBUILD: cutoff during water acceptor search = 7.5000
HBUILD: H , , placed for donor 2 THR N .
HBUILD: H , , placed for donor 3 THR N .
HBUILD: H , , placed for donor 4 VAL N .
HBUILD: H , , placed for donor 5 SER N .
HBUILD: H , , placed for donor 6 GLU N .
HBUILD: H , , placed for donor 8 ALA N .
HBUILD: H , , placed for donor 10 SER N .
HBUILD: H , , placed for donor 11 CYS N .
HBUILD: H , , placed for donor 12 VAL N .
HBUILD: H , , placed for donor 13 THR N .
HBUILD: H , , placed for donor 14 LEU N .
HBUILD: H , , placed for donor 15 TYR N .
HBUILD: H , , placed for donor 16 GLN N .
HBUILD: H , , placed for donor 17 SER N .
HBUILD: H , , placed for donor 18 TRP N .
HBUILD: HE1 , , placed for donor 18 TRP NE1 .
HBUILD: H , , placed for donor 19 ARG N .
HBUILD: HE , , placed for donor 19 ARG NE .
HBUILD: H , , placed for donor 20 TYR N .
HBUILD: H , , placed for donor 21 SER N .
HBUILD: H , , placed for donor 22 GLN N .
HBUILD: H , , placed for donor 23 ALA N .
HBUILD: H , , placed for donor 24 ASP N .
HBUILD: H , , placed for donor 25 ASN N .
HBUILD: H , , placed for donor 26 GLY N .
HBUILD: H , , placed for donor 27 CYS N .
HBUILD: H , , placed for donor 28 ALA N .
HBUILD: H , , placed for donor 29 GLU N .
HBUILD: H , , placed for donor 30 THR N .
HBUILD: H , , placed for donor 31 VAL N .
HBUILD: H , , placed for donor 32 THR N .
HBUILD: H , , placed for donor 33 VAL N .
HBUILD: H , , placed for donor 34 LYS N .
HBUILD: H , , placed for donor 35 VAL N .
HBUILD: H , , placed for donor 36 VAL N .
HBUILD: H , , placed for donor 37 TYR N .
HBUILD: H , , placed for donor 38 GLU N .
HBUILD: H , , placed for donor 39 ASP N .
HBUILD: H , , placed for donor 40 ASP N .
HBUILD: H , , placed for donor 41 THR N .
HBUILD: H , , placed for donor 42 GLU N .
HBUILD: H , , placed for donor 43 GLY N .
HBUILD: H , , placed for donor 44 LEU N .
HBUILD: H , , placed for donor 45 CYS N .
HBUILD: H , , placed for donor 46 TYR N .
HBUILD: H , , placed for donor 47 ALA N .
HBUILD: H , , placed for donor 48 VAL N .
HBUILD: H , , placed for donor 49 ALA N .
HBUILD: H , , placed for donor 51 GLY N .
HBUILD: H , , placed for donor 52 GLN N .
HBUILD: H , , placed for donor 53 ILE N .
HBUILD: H , , placed for donor 54 THR N .
HBUILD: H , , placed for donor 55 THR N .
HBUILD: H , , placed for donor 56 VAL N .
HBUILD: H , , placed for donor 57 GLY N .
HBUILD: H , , placed for donor 58 ASP N .
HBUILD: H , , placed for donor 59 GLY N .
HBUILD: H , , placed for donor 60 TYR N .
HBUILD: H , , placed for donor 61 ILE N .
HBUILD: H , , placed for donor 62 GLY N .
HBUILD: H , , placed for donor 63 SER N .
HBUILD: H , , placed for donor 64 HIS N .
HBUILD: HD1 , , placed for donor 64 HIS ND1 .
HBUILD: HE2 , , placed for donor 64 HIS NE2 .
HBUILD: H , , placed for donor 65 GLY N .
HBUILD: H , , placed for donor 66 HIS N .
HBUILD: HD1 , , placed for donor 66 HIS ND1 .
HBUILD: HE2 , , placed for donor 66 HIS NE2 .
HBUILD: H , , placed for donor 67 ALA N .
HBUILD: H , , placed for donor 68 ARG N .
HBUILD: HE , , placed for donor 68 ARG NE .
HBUILD: H , , placed for donor 69 TYR N .
HBUILD: H , , placed for donor 70 LEU N .
HBUILD: H , , placed for donor 71 ALA N .
HBUILD: H , , placed for donor 72 ARG N .
HBUILD: HE , , placed for donor 72 ARG NE .
HBUILD: H , , placed for donor 73 CYS N .
HBUILD: H , , placed for donor 74 LEU N .
------------------------- end of generate.log ----------------
--
Marilyn Yoder phone: 816-235-1986
School of Biological Sciences fax: 816-235-5158
Division of Cell Biology and Biophysics
University of Missouri-Kansas City e-mail myoder at cctr.umkc.edu
5100 Rockhill Rd
Kansas City, MO 64110-2499
