AMBER Archive (2008)

Subject: AMBER: Cysteine sulphonic acid parameters

From: Rima Chaudhuri (
Date: Wed Apr 30 2008 - 17:48:42 CDT

The protein-ligand complex that I am trying to simulate has an oxidized
cysteine residue in its sulphonic acid form (Cys-SO3). I built a CYO.lib
file for this non-standard residue using the following commands in tleap:
CYO = loadmol2 CYO.mol2
set CYO name "CYO"
set CYO head CYO.1.N
set CYO tail CYO.1.C
set CYO.1 connect0 CYO.1.N
set CYO.1 connect1 CYO.1.C
set CYO.1 restype protein
set CYO.1 name "CYO"
# set FF atom types
set CYO.1.N type N
set CYO.1.H type H
set CYO.1.CA type CT
set CYO.1.HA type H1
set CYO.1.C type C
set CYO.1.O type O
set CYO.1.CB type CT
set CYO.1.HB1 type H1
set CYO.1.HB2 type H1
set CYO.1.SG type S
set CYO.1.OD1 type O
set CYO.1.OD2 type O
set CYO.1.OD3 type O
saveoff CYO CYO.lib

However I realize that the Sulphur here should have a valence of 6, a) I do
not know the amber atom type is for S6?..I do not think naming the SG as 'S'
will suffice in this case!
When I try to add bonds between the Sulphur and Oxygen atoms (OD1, OD2 and
OD3) , it gives me error for the last bond between: > bond test.112.10
test.112.13 where residue 112 is my oxidized cysteine, atom 10 is SG and
atom 13 is OD3.
Error is :
Bond: maximum coordination exceeded on .R<CYO 112>.A<SG 10>
      -- setting atoms pert=true overrides default limits

I need help in generating the parameter files for this residue! please point
out what i might be doing wrong and if there are any alternate ways ? Also,
attached are the pdb file for UNIT test and the mol2 file CYO.mol2 that was
used for the lib file generation.



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