[gmx-users] Re: problem with pdb2gmx and ffG43a1p

[Ambrish]

Hi
I am using  ffG43a1p by Graham Smith which already has a definition for SEP
(phosphorylated Serine).
Best
Ambrish

On 8/3/07, Xavier Periole <X.Periole at rug.nl> wrote:
>
>
> the phosphorilated Ser is not defined in the G43a1 force field.
>
> You must define it. See manual for instructiion.
>
> XAvier
>
> > I am trying to perform simulation of a phosphorylated protein (phos. on
> a
> > Ser residue). I am tring to use  *ffG43a1p as my forcefield.
> > When I add a phosphate to the Ser, modify SER to SEP and run pdb2gmx it
> > gives me this :
> > ***
> > WARNING: atom HG1 is missing in residue THR 1 in the pdb file
> >         You might need to add atom HG1 to the hydrogen database of
> residue
> > THR
> >         in the file ff???.hdb (see the manual)
> >
> >
> > WARNING: atom H is missing in residue SEP 2 in the pdb file
> >         You might need to add atom H to the hydrogen database of residue
> > SEP
> >         in the file ff???.hdb (see the manual)
> >
> > -------------------------------------------------------
> > Program pdb2gmx, VERSION 3.3.1
> > Source code file: add_par.c, line: 221
> >
> >Fatal error:
> > Atom NE21 not found in rtp database in residue GLN, it looks a bit like
> NE2
> > -------------------------------------------------------
> >
> > *Same protein without the phosphate and OPLS forcefield  does not throws
> any
> > error.I have checked my pdb file and there is no NE21 in that.
> > If any one has done a simulation with a phosphorylated protein using
> > **ffG43a1p,
> > then a sample pdb file would be very helpful and appreciated.*
> > *
> > Best,
> > *--
> > Ambrish Roy
> >
> > Graduate Student
> > Bioinformatics Center
> > University of Kansas
> > 2030 Becker Dr
> > Lawrence, KS 66047
>
> -----------------------------------------------------
> XAvier Periole - PhD
>
> 1- Institute of Molecular Assemblies
>       City University of New York - USA
> 2- Molecular Dynamics-Group
>       University of Groningen - The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
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-- 
Ambrish Roy

Graduate Student
Bioinformatics Center
University of Kansas
2030 Becker Dr
Lawrence, KS 66047
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