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

[OZGE ENGIN]

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.

-----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
> _______________________________________________
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



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

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
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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