I am sorry if I did not frame the question correctly, but putting it very simply, is there a way to use capping residues with the charmm forcefield if the residues are --COCH3 and NHCH3?
On Thu, Jul 1, 2010 at 4:58 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sai Pooja wrote: > >> Would it be possible to add some capping residues (like --COCH3 and >> --NHCH3) by writing a separate .itp file and including it in the topology >> file? Is there a way to make it consistent with charmm forcefield? >> >> > No, because you have to specify bonds between these capping residues and > your protein. If you're #including them as new [moleculetypes], then you > can't add these bonds. > > > Can this be done alternatively by modifying the .rtp file? If yes, what >> other operations must one do before using these .rtp files? >> >> > Reading in the manual about the file format? I don't understand your > question entirely. All the other force fields use .rtp entries for caps, so > I don't see why this couldn't be done. > > -Justin > > > -- > ======================================== > > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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