Then try the option -ignh which ignores the hydrogens from the
pdb file and places them for you. They must be defined in ffxxx.hdb.
I am using ffG43a1p by Graham Smith which already has a definition for SEP
(phosphorylated Serine).
Best
Ambrish
On 8/3/07, Xavier Periole <[EMAIL PROTECTED]> 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
-----------------------------------------------------
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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