Quoting [EMAIL PROTECTED]: > Hello all, > > I have a protein with missing N- and C- terminus residues. I am > simulating a complex. To avoid in-silico charge interactions at the > wrong places due to the missing residues I have performed acetylation > and amidation. > > > When running pdb2gmx (GMX331) I experience a problem - > > > pdb2gmx -f blah.pdb -o blah.gro -p blah.top -water spc -ter -ignh -merge
Are you choosing 'none' for your termini? -Justin > > > Fatal error: > Atom H not found in residue 177 while adding improper > > > 177 is the number of the NH2 cap after re-numbering of the pdb file. > > > EXTRACT FROM THE PDB FILE - > > ..... > ATOM 1382 N NH2 A 181 15.061 41.575 44.283 0.00 0.00 > N > ATOM 1383 H1 NH2 A 181 14.812 41.813 45.232 0.00 0.00 > H > ATOM 1384 H2 NH2 A 181 16.038 41.447 44.027 0.00 0.00 > H > .... > > > The ffG53a6.rtp has the NH2 as - > > > [ NH2 ] > [ atoms ] > N NT -0.83 0 > H1 H 0.415 0 > H2 H 0.415 0 > [ bonds ] > N H1 gb_2 > N H2 gb_2 > -C N gb_9 > [ angles ] > -O -C N ga_33 > -CA -C N ga_19 > -C N H1 ga_23 > -C N H2 ga_23 > H1 N H2 ga_24 > [ dihedrals ] > -CA -C N H1 gd_14 > [ impropers ] > -C -O N -CA gi_1 > N H H -C gi_1 > > > Am I missing something? > > I reproduce this error with GMX332. > > However, if I use pdb2gmx with v3.2.1, pdb2gmx does not complain ! > > > Does anyone have any ideas/fixes? > > > Cheers > > Mitch > > > > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
