[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
