that makes sense, thank you Justin On Tue, Jun 1, 2010 at 4:01 PM, Justin A. Lemkul <[email protected]> wrote:
> > > maria goranovic wrote: > >> I tried pdb2gmx with an alanine pdb file, with options 5 (opls force >> field), 0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp on >> the output from pdb2gmx, I get a total charge of -1.1. Any ideas why this >> happens? >> >> The same problem is not there if one looks at a dipeptide. Why the problem >> for a single amino acid? It looks like when pdb2gmx applies patches for the >> N-terminus and C-terminus to the ends of a protein, it changes atom types >> for the peptide backbone. If one uses a single amino acid, the patches are >> applied to the same residue, and hence the odd -1.1 charge? If this is so, >> is this not a bug? >> >> > This is not a bug. You're choosing the wrong termini. With OPLS, there is > a "zwitterion" terminus option that you should be using, since a single > amino acid with two charged termini is a zwitterion. > > -Justin > > > Thank you for inputs, >> >> -maria >> >> >> -- >> Maria G. >> Technical University of Denmark >> Copenhagen >> >> > -- > ======================================== > > 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/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/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
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