On Wed, 27 Mar 1996, Ashley Buckle wrote:
> We are trying to refine a CIS peptide bond (not Pro) by first patching
> it as CISP (as in the manual), but without success - XPLOR flips it to
> trans every time and we dont really understand how to solve this. Has
> anyone actually refined a protein structure with a CIS (non-Pro)
> peptide bond?
I made the same observation that x-plor changed a cis-peptide bond (in
my case ASN) to trans. In my parameter file there is the statement :
dihe X C NH1 X 1250.0 1 0.0 ! always trans
which apparently forces all peptides to be in the cis configuration
except for PRO because ATOM N is of TYPE N ( not NH1) .
Because I also have "normal" trans-ASN I defined a new residue name (CAS)
for the residue with a cis-peptide bond. Note that a new atom type has
been assigned to ATOM N in CAS : ATOM N TYPE=NH4
This worked for me just fine.
Here is what I changed in the parameter and topology files :
{ =================================
These are the changes I made in
parhcsdx_ace.pro
================================= }
bond C NH4 3020.408 1.329 ! 0.014
bond CH1E NH4 1639.889 1.458 ! 0.019
bond H NH4 405.0 0.98 !*
! LE: ANGLE CH1E C NH4 20.0 117.5
angle CH1E C NH4 485.856 116.200 !2.0
! LE: CAS ANGLE NH4 C O 65.0 121.0
angle NH4 C O 759.150 123.000 !1.6
! LE : CAS ANGLE C CH1E NH4
angle C CH1E NH4 247.886 111.200 !2.8
angle CH1E CH1E NH4 672.465 111.500 !1.7 *
! LE: ANGLE CH2E CH1E NH4 65.0 110.0
angle CH2E CH1E NH4 672.465 110.500 !1.7
! LE: CAS ANGLE C NH4 CH1E 77.5 120.0
angle C NH4 CH1E 599.823 121.700 !1.8
angle C NH4 H 30.0 120.0 !* LE: CAS
angle CH1E NH4 H 35.0 120.0 !* LE: CAS
! LE: dihedrals and improper
dihe X C NH4 X 1250.0 2 180.0 ! LE: CAS double minimum CIS !
dihe X CH1E NH4 X 0.9 3 0.0 ! LE: CAS
impr C X X NH4 300.0 0 0.0 ! LE: CAS
impr NH4 X X H 135.0 0 0.0 ! LE: CAS
impr NH4 X X NH4 75.0 0 0.0 ! LE: CAS (for CAS-CAS )
impr NH4 X X NR 75.0 0 0.0 ! LE: CAS (for CAS-X )
NONBonded NH4 0.2384 2.8509 0.2384 2.8509 ! LE: CAS
{ ===============================
These are the changes I made in
tophcsdx_ace.pro
=============================== }
MASS NH4 14.00670! LE: Atom type definition for CIS ASN (CAS)
!---------------------------- LE: CIS ASN --------------------------------
! Changes : 2-10-96 ATOM N TYPE=NH1 -> ATOM N TYPE NH4
!-------------------------------------------------------------------------
RESIdue CAS
GROUp
ATOM N TYPE=NH4 CHARge=-0.35 END
ATOM H TYPE=H CHARge= 0.25 END
ATOM CA TYPE=CH1E CHARge= 0.10 END
ATOM CB TYPE=CH2E CHARge= 0.00 END
ATOM CG TYPE=C CHARge= 0.55 END !#
ATOM OD1 TYPE=O CHARge=-0.55 END !#
ATOM ND2 TYPE=NH2 CHARge=-0.60 END !#
ATOM HD21 TYPE=H CHARge= 0.30 END !#
ATOM HD22 TYPE=H CHARge= 0.30 END !#
ATOM C TYPE=C CHARge= 0.55 END !#
ATOM O TYPE=O CHARge=-0.55 END !#
BOND N CA
BOND CA C
BOND C O
BOND N H
BOND CA CB
BOND CB CG
BOND CG OD1
BOND CG ND2
BOND ND2 HD21
BOND ND2 HD22
DIHEdral N CA CB CG
DIHEdral CA CB CG OD1
DIHEdral CB CG ND2 HD21
IMPRoper CA N C CB !tetrahedral CA
IMPRoper CG OD1 ND2 CB !planar CG
IMPRoper ND2 HD21 HD22 CG !planar ND2
DONOr H N
DONOr HD21 ND2
DONOr HD22 ND2
ACCEptor OD1 CG
ACCEptor O C
END {CAS}
!------------------------------------------------------------------
Hope that helps.
Lothar Esser
-------------------------------------------------------------------
Dr. Lothar Esser
Howard Hughes Medical Institute
5323 Harry Hines Blvd.
Dallas Texas 75235-9050
e-mail : esser at chop.swmed.edu
