Sorry, clicked 'send' too soon. How was this version of Gromacs compiled? I remember submitting a bugzilla not too long ago about a similar problem, and it ended up being that the Ubuntu package was broken. Re-compiling from source fixed the problem. The -ter response was a knee-jerk reaction, as a related problem is somewhere in the list archive.
-Justin Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > 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 > ======================================== 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
