Thanks Justin. It worked perfectly. Chandan
-- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Chandan Choudhury wrote: > >> Hello gmx-users >> >> I am trying to simulate an amino acid (say GLN). It can be as a >> zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields >> has a complete parameter for them. While in ffamber, I have the >> > > This is not true. OPLS can handle isolated amino acids, you just have to > manually choose the termini in pdb2gmx (using -ter). Use the "zwitterion" > forms of the termini, since in fact, you have a zwitterion. > > -Justin > > > parameters for CGLU and NGLU, but not for a Glutamine. Do I need to define >> it there, or there is some way out. If I need to define it, how do I retrive >> the partial charges. >> >> Any insight would be very helpful. >> Thanks >> >> Chandan >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> > -- > ======================================== > > 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 gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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