http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Janowicz, Adrianna C. > Sent: Tuesday, 22 November 2011 8:08 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] UNK not found > > The following is a part of a .pdb file I generated. > > > HETATM 250 C1 UNK 1 18.454 11.417 22.519 1.00 0.00 > C > HETATM 251 C2 UNK 1 19.297 10.247 22.595 1.00 0.00 > C > HETATM 252 C3 UNK 1 19.949 9.511 21.410 1.00 0.00 > C > HETATM 253 C4 UNK 1 20.244 8.034 21.669 1.00 0.00 > C > HETATM 254 C5 UNK 1 21.458 7.527 21.887 1.00 0.00 > C > HETATM 255 C6 UNK 1 22.793 8.230 22.144 1.00 0.00 > C > HETATM 256 C7 UNK 1 22.749 9.752 22.264 1.00 0.00 > C > HETATM 257 C8 UNK 1 23.873 10.420 23.098 1.00 0.00 > C > HETATM 258 H1 UNK 1 22.039 6.693 21.885 1.00 0.00 > H > HETATM 259 H2 UNK 1 19.416 7.379 21.609 1.00 0.00 > H > > ... etc. > > I'm getting an UNK not found in residue topology error message. > After I run > pdb2gmx -f XXX.pdb -o conf.pdb > > Fatal error: > Residue 'UNK' not found in residue topology database > > I tried replacing UNK with H and C, respectively, and still got the > same > error except with "Residue 'H' not...". > > What do I replace the UNK with to run the file smoothly or how do I add > the unknown atom types so that the command runs? > > Thanks! > > > > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
