I want to do energy minimization of a small peptide (19 residues long) file (in pdb format).
Can you please tell which tutorial is best for this purpose and which force field should I use. Thanks Kumud Agarwal On Tue, Jan 24, 2012 at 10:43 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > kumud agarwal wrote: > >> I tried to use the command pdb2gmx >> >> *kumud@ubuntu:~/gromacs/**gromacs-4.5.5/share/tutor/**mciz$ pdb2gmx >> -ignh -ff G43a1 -f mciz.pdb -o mciz.gro -p mciz.top* >> >> >> At the end the message came as >> >> *Program pdb2gmx, VERSION 4.5.5 >> >> Source code file: pdb2top.c, line: 239 >> >> Fatal error: >> Could not find force field 'G43a1' in current directory, install tree or >> GMXDATA path.* >> >> >> What is the problem here? >> >> > The naming of force fields is different in the 4.5.x series. Whatever > tutorial you're looking at is outdated. Try one of the updated ones on the > Gromacs website, or just choose the force field interactively. > > -Justin > > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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