I've moved on from that point; now I'm stuck at where it asks me to remove molecules of solvent from the topology file.
On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hey :) > > Sorry for replying a bit late. But the issues you mention in this and the > other posts are usually solved by closely reading the text of the tutorial, > not only the commands. > > Cheers, > > Tsjerk > > > On Sun, Aug 25, 2013 at 3:44 AM, The One And Only <chappybo...@gmail.com > >wrote: > > > Never mind, I'm dumb. I just realized that protein.pdb means i have to > > specify which protein i want like "1qlz.pdb" and not actually type > > "protein.pdb" BUT THANKS GUYS!! > > > > > > On Sat, Aug 24, 2013 at 6:40 PM, The One And Only <chappybo...@gmail.com > > >wrote: > > > > > so how do i solve the protein.pdb issue? > > > > > > > > > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > > > > >> > > >> > > >> On 8/24/13 9:26 PM, The One And Only wrote: > > >> > > >>> that's something i know nothing about; I just graduated from high > > school > > >>> and I have no background or experience in open source projects or > > >>> programs > > >>> like pymol/gromacs. My professor wants me to be able to produce a > > setup, > > >>> simulation, and analysis within a week so I'm pretty desperate right > > now > > >>> in > > >>> terms of getting help. Do you know how to get the right .pdb file in > my > > >>> working directory? > > >>> > > >>> > > >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux > > >> tutorial. Google can find lots of good ones. Producing a quality > > >> simulation cannot be rushed, and if you don't know the fundamentals of > > >> navigating the command line and directory structure, it's nearly > > >> impossible. You need to invest time in learning the environment > before > > >> doing anything, I'm afraid. Just to give a bit of perspective, we > used > > to > > >> train our undergrads for nearly a full semester (at least 2-3 months) > > >> before requiring them to do any "real" work. At least a week or two > of > > >> that time was spent getting used to command line and Linux in general. > > >> > > >> -Justin > > >> > > >> -- > > >> ==============================**==================== > > >> > > >> Justin A. Lemkul, Ph.D. > > >> Postdoctoral Fellow > > >> > > >> Department of Pharmaceutical Sciences > > >> School of Pharmacy > > >> Health Sciences Facility II, Room 601 > > >> University of Maryland, Baltimore > > >> 20 Penn St. > > >> Baltimore, MD 21201 > > >> > > >> jalemkul@outerbanks.umaryland.**edu < > jalem...@outerbanks.umaryland.edu>| > > (410) > > >> 706-7441 > > >> > > >> ==============================**==================== > > >> -- > > >> 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> > > >> > > > > > > > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 > -- 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
