Thank you Justin, You noticed well that. But this example was built to work without -ignh and to exemplify my problem, because in real case I have this protein and either I can use 'sed' to fix it (mainly H names) I found it annoying sometimes, so why not -ignh?
Cheers, Alan On Mon, Jun 15, 2009 at 15:51, <gmx-users-requ...@gromacs.org> wrote: > Alan wrote: >> Hi there, >> I am trying to understand why when doing: >> >> pdb2gmx -f GGG.pdb -ff amber99sb -ignh >> >> I am getting: >> >> WARNING: atom H is missing in residue GLY 2 in the pdb file >> You might need to add atom H to the hydrogen database of residue GLY >> in the file ff???.hdb (see the manual) >> > > I don't know why this is failing, but from the looks of your .pdb file, you > have > all the atoms you need, properly named and everything. Why do you need -ignh? > > -Justin > >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 4.0.5 >> Source code file: pdb2top.c, line: 704 >> Fatal error: >> There were 1 missing atoms in molecule Protein_G, if you want to use >> this incomplete topology anyhow, use the option -missing >> ------------------------------------------------------- >> >> in /sw/share/gromacs/top/ffamber99sb.hdb I have: >> >> GLY 2 >> 1 1 H N -C CA >> 2 6 HA CA N C >> >> And I see nothing wrong with that. >> >> in /sw/share/gromacs/top/ffamber99sb.rtp: >> >> [ GLY ] >> [ atoms ] >> N amber99_34 -0.41570 1 >> H amber99_17 0.27190 2 >> CA amber99_11 -0.02520 3 >> HA1 amber99_19 0.06980 4 >> HA2 amber99_19 0.06980 5 >> C amber99_2 0.59730 6 >> O amber99_41 -0.56790 7 >> >> Which is pretty OK too. >> >> Besides, I don't get any error for NGLY or CGLY. Only "atom H is >> missing in residue GLY 2". If I mess with ffamber99sb.hdb for GLY I >> got others messages stating the other missing atoms. >> OPLS, which is very similar, works fine. >> >> The pdb is as simple as this: >> ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 >> ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 >> ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 >> ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 >> ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 >> ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 >> ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 >> ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 >> ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 >> ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 >> ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 >> ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 >> ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 >> ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 >> ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 >> ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 >> ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 >> ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 >> ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 >> ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 >> ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 >> ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 >> ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 >> ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 >> >> >> My memory may fail, but I can swear it was working before... >> >> Many thanks in advance, >> Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< _______________________________________________ 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
