Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this "H" is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those.
This is the residue in question ATOM 1 N GLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA GLU 32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C GLU 32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O GLU 32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB GLU 32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG GLU 32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD GLU 32 -18.573 11.627 -1.334 1.00 0.00 C ATOM 8 OE1 GLU 32 -19.009 12.797 -1.488 1.00 0.00 O ATOM 9 OE2 GLU 32 -18.089 11.174 -0.257 1.00 0.00 O ATOM 10 HA GLU 32 -18.845 8.057 -3.227 1.00 0.00 H ATOM 11 HB1 GLU 32 -20.805 10.368 -2.695 1.00 0.00 H ATOM 12 HB2 GLU 32 -20.026 9.493 -1.358 1.00 0.00 H ATOM 13 HG1 GLU 32 -17.724 10.072 -2.453 1.00 0.00 H ATOM 14 HG2 GLU 32 -18.628 11.255 -3.435 1.00 0.00 H ATOM 15 HT2 GLU 32 -19.381 9.526 -5.140 1.00 0.00 H ATOM 16 HT1 GLU 32 -20.892 8.644 -5.172 1.00 0.00 H [boinc...@vps test]$ grep -A5 "GLU" /usr/local/gromacs/share/gromacs/top/ffamber99sb.* /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb:GLU 4 /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 1 H N -C CA /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 5 HA CA N CB C /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HB CB CA CG /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HG CG CB CD /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-ASP 3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad:[ GLU ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- [ atoms ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- N amber99sb_34 -0.51630 1 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- H amber99sb_17 0.29360 2 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- CA amber99sb_11 0.03970 3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- HA amber99sb_19 0.11050 4 On Mon, Nov 9, 2009 at 4:26 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Jack Shultz wrote: >> >> I tried to protonate my pdb file using openbabel >> babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h >> >> Then I ran pdb2gmx with the following >> >> pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p >> Protein.top -water spce -ignh >> >> But apparently I am missing a H from my first residue. Is there an >> easy way to add missing atoms? > > Yep - you may need a well-formatted .hdb file, like the message says :-) You > should check out whether the AMBER port you installed supports this feature > or not. Alternatively, have a look in the file and with a viewer to see what > is present for residue 1 and how the atoms are named, and whether renaming > some atoms will fix the issue. > > Mark > >> WARNING: atom H is missing in residue GLU 1 in the pdb file >> You might need to add atom H to the hydrogen database of residue >> GLU >> in the file ff???.hdb (see the manual) >> >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 4.0.5 >> Source code file: pdb2top.c, line: 704 >> >> Fatal error: >> There were 1 missing atoms in molecule Protein, if you want to use >> this incomplete topology anyhow, use the option -missing >> ------------------------------------------------------- >> > -- > gmx-users mailing list gmx-us...@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 > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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