[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 UNK1 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 listgmx-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
Re: [gmx-users] UNK not found
Janowicz, Adrianna C. wrote: 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 UNK1 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? Please make use of the list archive and Gromacs website. This error, in many forms, has been asked and answered a thousand times over. Moreover: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-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
RE: [gmx-users] UNK not found
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 UNK1 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 listgmx-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 listgmx-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] UNK not found in residue topology
Hello, 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 figured out what the error was and tried to add UNK as carbon to ffopslaa.rtf [UNK] [ atoms ] UNK UNK 0.000 0 but I am still getting the same error. What do I do? Adrianna -- gmx-users mailing listgmx-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
Re: [gmx-users] UNK not found in residue topology
Janowicz, Adrianna C. wrote: Hello, 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 figured out what the error was and tried to add UNK as carbon to ffopslaa.rtf There are no .rtf files used by Gromacs, so if you've created or edited one, it will have no effect. [UNK] [ atoms ] UNK UNK 0.000 0 but I am still getting the same error. What do I do? In theory, one can define a residue named UNK with atom names and types of UNK, but that's an incredibly awkward mechanism. It would probably be worthwhile to use real, existing atom types (which would be required by OPLS) with a meaningful residue name. Perhaps the format of your .pdb file is wrong and pdb2gmx is reading another column for the residue name instead of the one intended. If you specify everything as UNK, you'll never know. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-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] UNK not found in residue topology
Hello, I'm getting an UNK not found in residue topology error message. I figured out what the error was and tried to add carbon to ffopslaa.rtf but it was unsucessful. What can I do/How can I change my pdb file from UNK so that Carbon and Hydrogen can be recognized? (I built my own hydrocarbon strucutre and added it to an existing PDB file). Thanks, Adrianna -- gmx-users mailing listgmx-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
Re: [gmx-users] UNK not found in residue topology
Janowicz, Adrianna C. wrote: Hello, I'm getting an UNK not found in residue topology error message. I figured out what the error was and tried to add carbon to ffopslaa.rtf but it was unsucessful. What can I do/How can I change my pdb file from UNK so that Carbon and Hydrogen can be recognized? (I built my own hydrocarbon strucutre and added it to an existing PDB file). I think you need to be a bit more specific about what you're trying to do. Are you getting errors from pdb2gmx or some other tool? If so, what are they? Otherwise, the only requirement for proper processing is that the PDB format be retained and that the atom names match what is expected in the .rtp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-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
