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

[Justin A. Lemkul]

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

> 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 :)

So have I got it correct that you truncated the N-terminus originally, and are
now adding residues back?  It still suggests to me that you've generated a poor
starting structure; the nomenclature should not be causing the issue.  Identify
which bonds pdb2gmx is warning you about (and the atoms involved), and evaluate
them with a viewer (VMD, etc).  Likely the model you've constructed has some
non-physical attributes.

-Justin

>
> 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
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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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/
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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>
>
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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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/

========================================