Re: [gmx-users] Amino acid simulation
Thanks Justin. It worked perfectly. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul 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 listgmx-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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] Amino acid simulation
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 listgmx-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
Re: [gmx-users] Amino acid simulation
It's highly unusual to simulate a single amino acid. I don't exactly know what's your purpose with it, but if you really want to do it, you need to generate those parameters. I know there are web services for generating gromos FF parameters for "unusual" molecules, possibly there are such resources for amber or opls too. On Mon, Apr 12, 2010 at 8:36 PM, 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 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 > > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
