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 <iitd...@gmail.com>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 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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