Thank you for your help Justin. I have corrected my naming problem in the pdb file. However, I am still getting errors. It does not seem to recognize the residues. BUT I dont actually have "residues" in my system, because I am not modeling a protein. So I am not sure what to put in the residue name column. Gromacs does work on molecules that are not proteins correct? My molecules are histidine like so I tried putting HIS as the residue name, but I got the error:
"Fatal error: Residue 'H' not found in residue topology database" When I dont put anything in that column I get the error: "Fatal error: Residue '' not found in residue topology database" And when I just generically call everything solvent and put SOL in that column I get: "Fatal error: Residue 'S' not found in residue topology database" You get the picture here. Does anyone have any solutions to my residue naming problem? Thank you. here is my pdb file: HETATM 1 CT 2 -4.438 3.334 2.988 HETATM 2 CT 2 0.588 3.313 0.517 HETATM 3 CT 2 5.476 3.310 -2.216 HETATM 4 HC 2 -4.134 2.590 3.731 HETATM 5 HC 2 -5.525 3.438 3.047 HETATM 6 HC 2 -3.996 4.291 3.276 HETATM 7 HC 2 1.480 3.111 1.117 HETATM 8 HC 2 -0.266 3.349 1.200 HETATM 9 HC 2 0.702 4.307 0.076 HETATM 10 HC 2 6.375 3.525 -1.633 HETATM 11 HC 2 4.648 3.862 -1.761 HETATM 12 HC 2 5.628 3.709 -3.223 HETATM 13 CT 2 -3.996 2.922 1.581 HETATM 14 HC 2 -2.902 2.862 1.545 HETATM 15 HC 2 -4.281 3.703 0.865 HETATM 16 CT 2 0.394 2.242 -0.557 HETATM 17 HC 2 -0.485 2.486 -1.167 HETATM 18 HC 2 1.250 2.252 -1.242 HETATM 19 CT 2 5.188 1.805 -2.247 HETATM 20 HC 2 6.018 1.286 -2.742 HETATM 21 HC 2 4.300 1.615 -2.864 HETATM 22 CT 2 -4.587 1.582 1.127 HETATM 23 HC 2 -5.682 1.638 1.161 HETATM 24 HC 2 -4.298 0.792 1.828 HETATM 25 CT 2 0.235 0.836 0.028 HETATM 26 HC 2 -0.616 0.818 0.720 HETATM 27 HC 2 1.117 0.581 0.625 HETATM 28 CT 2 4.981 1.206 -0.852 HETATM 29 HC 2 4.152 1.720 -0.350 Jacob Harvey On Sat, Apr 4, 2009 at 2:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jacob Harvey wrote: > >> Dear All, >> >> I am trying to use the OPLS-AA force field to model some imidazole >> containing compounds. I've noticed that imidazole units are referenced in >> the ffoplsaa.atp file as the following: >> >> opls_557 14.00670 ; N1 in imidazole >> opls_558 12.01100 ; C2 in imidazole >> opls_559 14.00670 ; N3 in imidazole >> opls_560 12.01100 ; C4 in imidazole >> opls_561 12.01100 ; C5 in imidazole >> opls_562 1.00800 ; H1 in imidazole >> opls_563 1.00800 ; H2 in imidazole >> opls_564 1.00800 ; H4 in imidazole >> opls_565 1.00800 ; H5 in imidazole >> >> But there are no parameters for these atoms in the ffoplsaa.rtp file. Does >> anyone know how I can go about naming these atoms in my pdb file? Thank you >> in advance. >> >> > Not every compound is present in a .rtp file. Check out its contents and > you'll see what it has - pretty much just amino acids. The charges on each > atom are not specific to an atom type, they are specific to a chemical > species for which the parameterization scheme has been conducted. > Lennard-Jones parameters are specified in ffoplsaanb.itp. > > I suggest a thorough read of Chapter 5 of the manual to understand the > contents of these database-type files, and how they are used in assembling a > topology. > > -Justin > > Jacob Harvey >> >> -- >> -- >> Jacob Harvey >> >> Graduate Student >> >> University of Massachusetts Amherst >> >> j.ha...@gmail.com <mailto:j.ha...@gmail.com> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > -- -- Jacob Harvey Graduate Student University of Massachusetts Amherst j.ha...@gmail.com
_______________________________________________ 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