On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: > On 4/01/2012 1:07 PM, Peter C. Lai wrote: > > 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... > > Correct, it doesn't. > > >> 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? > > Yes, you just make the path with your installed VMD libraries available > in the linking path, just like with FFTW or whatever. > > > Is there a configure flag that controls this? > > Yes. It's enabled by default, but there is no attempt to check that a > VMD installation exists. > > > and do you mean dlpolyplugin.so ? > > No. DLPOLY is a MDS program, IIRC.
No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 > > > > > Is there another tool with which I can do specific selections and write > > them out to something I can reinput into gromacs? > > > > Script g_select? > That sounds good. Although I may have a workaround by altering my procedure. -- ================================================================== 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