Thanks for your answer again. I will restrain the heavy atoms only first.
Best regards, lina ________________________________________ From: [email protected] [[email protected]] on behalf of Justin A. Lemkul [[email protected]] Sent: Wednesday, September 22, 2010 11:43 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: > Thanks for your answer. > > How can I tell which ones I should restrain? all no-H atoms? in most general > situations. For the sake of clarity in the archive, it's probably best to avoid broad generalizations. People can easily stumble upon a post and take it way out of context. A "general situation" might encompass a lot. I will reiterate that if you want to recapitulate the behavior of pdb2gmx with respect to typical biomolecules, you should choose all non-H atoms. If you have some other specialized application, I can make no recommendation, nor can anyone else, in the absence of a more thorough description. -Justin > > lina > ________________________________________ > From: [email protected] [[email protected]] on behalf > of Justin A. Lemkul [[email protected]] > Sent: Wednesday, September 22, 2010 11:15 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Position Restraints > > #ZHAO LINA# wrote: >> Hi, >> >> When I used the genrestr to get the posre.itp specially, >> I found it set all atom to be applied to. >> Is that okay? How could I figure out which ones should not be set to. >> >> A little naive questions, but I do do not know. > > The answer depends on your needs. When running genrestr without an index > file, > you can choose from any of the default groups. If you provide an index file, > any group can be chosen. > > The default behavior of pdb2gmx is to generate a posre.itp file that restrains > all heavy (non-H) atoms. You can do the same with genrestr if you want, but > again, the atoms you want to restrain depend on your goals. > > -Justin > >> Thanks with regards, >> >> lina >> > > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== 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 ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
