Dr. Justin Lemkul, >> Ah I see. I also noticed that in the original specbond.dat, the bond >> distance specification for the disulfide bonds between 2 CYS's or between 2 >> CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I >> still find a bit unclear is the final columns (residue rename). Is this what >> my specbond.dat file should look like? >>
>The final columns specify the new residue names that should be assigned to the >residues only in the case that a special bond was created. You'll see from the >existing Cys specifications that a residue named "CYS" (standard PDB >nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but >only if a special bond is created. The nomenclature exists because of the way >the force fields work. In your case, you don't need to rename anything, so >preserving the original residue names is the proper way to go. >Of course, the answer to "is this correct?" is generally obtained by running >it ;) >> 3 >> CYS N 1 VAL C 1 0.132 CYS VAL >> CYS SG 1 CYS SG 1 0.20 CYS2 CYS2 >> CYM SG 1 CYM SG 1 0.20 CYS2 CYS2 With the above specbond.dat file in the working directory, I attempted the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp" and received this fatal error message (it is the same as the original): ------------------------------------------------------- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- -Matthew Stancea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.