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