[gmx-users] Error during grompp run

[Justin Lemkul]

On Wed, Mar 20, 2013 at 2:30 AM, Kshatresh Dutta Dubey
<kshatresh at ymail.com>wrote:

> Dear Justin,
>
> I checked for it several times and I am quite sure there is no typo error,
> permission problem and location of posre_Protein.itp file. Even, I run same
> job on different machines from beginning and I found same type of error.
>
>

Without seeing the relevant topology snippet, listing of files in the
working directory (ls -l), and the grompp command invoked, there's no way
for anyone to help you.  This should be a relatively easy fix.  The fact
that it does not work on multiple machines indicates there is indeed a
problem with either the file name or the manner in which it is included in
the topology.  What is posre_Protein.itp?  What it written by pdb2gmx with
a nonstandard name or was it something you created?

-Justin


>   ------------------------------
> *From:* Justin Lemkul <jalemkul at vt.edu>
> *To:* Kshatresh Dutta Dubey <kshatresh at ymail.com>; Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, March 19, 2013 10:48 PM
> *Subject:* Re: [gmx-users] Error during grompp run
>
>
>
> On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey <
> kshatresh at ymail.com> wrote:
>
> Dear Users
>
> I am using groamcs 4.4.4 and when I run grompp during equilibration
> process, it closes with error
>  " Fatal error:Topology include file "posre_Protein.itp" not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors"
>
> However, I found Topology include file "posre_Protein.itp" in current
> directory. I am able to successfully run previous grompp
> during minimization, but I am facing this problem during equilibration only.
>
> Please help me to get rid of this issue. I welcome all suggestions.
>
>
> If grompp says it's not there, it's not there.  Check carefully for typos
> in file names or #include statements as well as read permissions on the
> file itself.
>
> -Justin
>
> --
>
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
>
>


-- 

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

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

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