On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: > On 4/01/2012 12:30 PM, Peter C. Lai wrote: > > I used VMD to process a gro file and wrote it to pdb, because VMD can't > > write gro files. Because the # of residues exceeds 9999, it numbered the > > remaining residues in the PDB in 4 bit hex. Editconf will not convert the > > hex numbered residue ids back to decimal (it just truncates anything past > > the final 0-9 digit in the field). Does this mean if I feed the pdb as-is > > into grompp it will also have problems reading the residue numbers? > > > > Gromacs 4.5.3 > > > > Yes. VMD is writing non-standard-compliant PDB. Blame it. >
Does the PDB format even support residue numbers > 9999? I thought the resid field was fixed at 4 digits... > If you've linked GROMACS to the dlopen library from VMD (the default) > then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Is there a configure flag that controls this? and do you mean dlpolyplugin.so ? Is there another tool with which I can do specific selections and write them out to something I can reinput into gromacs? -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
