On Wed, Mar 20, 2013 at 2:30 AM, Kshatresh Dutta Dubey <kshatr...@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 <jalem...@vt.edu> > *To:* Kshatresh Dutta Dubey <kshatr...@ymail.com>; Discussion list for > GROMACS users <gmx-users@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 < > kshatr...@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists