Re: AMBER: Cysteine sulphonic acid parameters

From: David A. Case <>
Date: Wed, 30 Apr 2008 17:06:02 -0700

On Wed, Apr 30, 2008, Rima Chaudhuri wrote:

> 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!

You probably do need to define a new atom type, and the corresponding force
field parameters. You already seem to have charges in the mol2 file; I'm not
sure where they came from, but it looks like a good start. Beyond that, you
probably just need to define bond lengths and angles for SO-O, O-SO-O, and
O-SO-CT and SO-CT-H1 to get bond lengths and angle correct for a sufonic acid
group. (I using "SO" for the new sulfur type here.)

[Note that, instead of all the "set type" commands above, you could just edit
the CYO.mol2 file, and put the types in the file itself.]

> 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

The bonds between sulfur and the OD1,OD2,OD3 atoms are already in the mol2
file. So you don't need to "add" them, and trying to do so probably causes
the program to think that SG has too many bonds.

Use the "desc CYO.1" or "desc CYO.1.SG" (etc.) commands to see what bonds you
have. Or, use the visualizer in xleap. You should see that the bonds are
already there.

...good luck...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun May 04 2008 - 06:07:15 PDT
Custom Search