[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

[OZGE ENGIN]

Ok, it should be better to describe the problem in a more detailed way. 
I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about the nomenclature of the N terminus. I read things in the link, searched the web and made some discussion with my friend, but I could not find the source of the error :)

Thank you Justin

-----Original Message-----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Mon, 31 Mar 2008 15:25:11 -0400
Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Quoting OZGE ENGIN <OZENGIN at KU.EDU.TR>:

> I already indicated the problem that I have. If I put an N prefix to the
> first residue, I get warning of having "long bonds." It has been indicated in
> the mail.Moreover, these long bonds can not be minimized during the
> minimization step. Although I put a relatively higher tolerance for the force
> on atoms.

Alright, that makes more sense.  You didn't say before that you couldn't resolve
the long bonds by minimization.  It seemed that you were asking again about the
N-terminal nomenclature.  It sounds like your starting structure has problems,
but without knowing more I can't comment on that.  Is it something you've
built, something from the RCSB, etc?

Have a look at your structure and the mdrun output (md.log, in particular) to
see if you can determine where things are falling apart based on specific
warnings (LINCS, etc.)

-Justin

>
> -----Original Message-----
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Mon, 31 Mar 2008 14:42:55 -0400
> Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
>
> Quoting OZGE ENGIN <OZENGIN at KU.EDU.TR>:
>
> > Hi all,
> >
> > I am trying to use AMBER ff in GROMACS. I have followed the steps that are
> > given in the  http://chemistry.csulb.edu/ffamber/  link.
> >
> > The first residue of the protein is GLN. I put an N prefix to this residue.
> > The pdg2gmx works well except giving an warning of long bond between some
> > atoms.
> >
> > In contrast, if I have not put any prefix to GLN, then, the following error
> > appears:
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > WARNING: atom H is missing in residue GLN 1 in the pdb file
> > You might need to add atom H to the hydrogen database of residue GLN
> > in the file ff???.hdb (see the manual)
> >
> > -------------------------------------------------------
> > Program pdb2gmx, VERSION 3.3.1
> > Source code file: pdb2top.c, line: 697
> >
> > Fatal error:
> > There were 1 missing atoms in molecule Protein, if you want to use this
> > incomplete topology anyhow, use the option -missing
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > I looked at both the .rtp and .hdb files, but everything seems to be
> correct.
> >
> > Does anybody face with a similar problem?
>
> If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e.,
> NGLN),
> and likewise for C-terminal residues, CXXX.  This is in the documentation
> from
> the AMBER ports at the link you cite above, and the link I already provided
> you.
>
> So what's the problem?
>
> -Justin
>
> >
> > Thanks in advance
> > Ozge Engin
> > =================================
> > Computational Science & Engineering
> > Koc University
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>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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>
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
> _______________________________________________
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================
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Ozge Engin
=================================
Computational Science & Engineering
Koc University