AMBER Archive (2008)

Subject: Re: AMBER: Cysteine sulphonic acid parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu May 01 2008 - 07:03:19 CDT

Quoting Rima Chaudhuri <rima.chaudhuri_at_gmail.com>:

> 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

I think you already checked if your new residue was in R.E.DD.B...
Just to be sure. See:
F-70 Central fragment of S-methyl-L-cysteine J. Pecher 11-04-2006
F-69 Central fragment of S-methyl-L-cysteine J. Pecher 11-04-2006
F-68 Central fragment of S-sulfonate-L-cysteine J. Pecher 11-04-2006
F-67 Central fragment of S-sulfonate-L-cysteine J. Pecher 11-04-2006
F-66 Central fragment of sulfonate-L-cysteine J. Pecher 11-04-2006
F-65 Central fragment of sulfonate-L-cysteine J. Pecher 11-04-2006

> 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.

If you are interested we can updated the R.E.DD.B. projects to add in
each project the corresponding frcmod file with missing force field
parameters.
This will correspond to the following links:
http://q4md-forcefieldtools.org/REDDB/up/"REDDB-code"/script3.ff
or
http://q4md-forcefieldtools.org/REDDB/up/F-66/script3.ff
http://q4md-forcefieldtools.org/REDDB/up/F-65/script3.ff

regards, Francois

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