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

[Xavier Periole]

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 <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

-----------------------------------------------------
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
-----------------------------------------------------