Thanks David and Francois.
I checked the database earlier and looked into F-65, but had no cues for why
amber was not recognizing the 'sx' atom type mentioned there for the
hypervalent Sulphur in the Sulfonate? I checked the leaprc.gaff in Amber and
there was a sx and sy atomtype for s4 and s6 respectively!
Either ways, Yes, updating the R.E.DD.B projects to include the frcmod files
would certainly be helpful. In the meanwhile I will work on David's
suggestion of creating a new atom type for the sulphur as SX or SO..
thanks,
-Rima
On Thu, May 1, 2008 at 7:03 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Quoting Rima Chaudhuri <rima.chaudhuri.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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Received on Sun May 04 2008 - 06:07:26 PDT
