[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
OZENGIN at KU.EDU.TR
Mon Mar 31 21:10:24 CEST 2008
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.
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
> In contrast, if I have not put any prefix to GLN, then, the following error
> 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
So what's the problem?
> Thanks in advance
> 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
jalemkul at vt.edu | (540) 231-9080
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