On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Ilya Chorny wrote: > >> I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached >> to the side chain nitrogen called ASBG. I want to test the new residue by >> itself. >> >> When I pdb2gmx it I get the following error. >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 4.0.3 >> Source code file: pgutil.c, line: 87 >> >> Fatal error: >> Atom N not found in residue 1094904186 while adding improper >> >> ------------------------------------------------------- >> >> > If the residue is by itself, something is seriously wrong if pdb2gmx is > detecting a billion residues! I'll checkmy file again. > > > If I comment out >> CA +N C O improper_O_C_X_Y >> >> > Right, because if the residue is by itself, there will be no N in the next > residue (+N). If this is true then pdb2gmx will crash evertime it is run on an isolated AA, which it doesn't. > > > Then pdb2gmx creates the gro and top with no error messages. >> >> I saw an much earlier post by Justin with a similar error message but no >> resolution. Anyone have anythoughts? >> >> > IIRC, that was in reference to version 3.3.1, which turned out to be the > result of a broken Ubuntu package, and was not a problem with Gromacs > itself. > > Try it in the context of the actual molecule, if topology construction > requires the next residue. In isolation, that residue will always fail with > +N. > > -Justin > > Thanks, >> >> Ilya >> >> >> >> >> -- >> Ilya Chorny Ph.D. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.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 >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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://www.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 > -- Ilya Chorny Ph.D.
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