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

[OZGE ENGIN]

Justin, thank you very much for your attention. This is totally my fault. After putting N to the first residue, the column that indicates the coordinates has been flipped to the right. So, the first numbers could not be read by pdb2gmx. That is the source of the problem. However, thank you again.


-----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 17:41:50 -0400
Subject: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in	GROMACS

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
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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
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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