On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote: > On 4/01/2012 2:19 PM, Peter C. Lai wrote: > > 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 > > Sorry, dlopen is the mechanism that allows the executing code to see if > a dynamic link library contains a function that delivers the required > functionality. So it's just a matter of having the VMD stuff in the > dynamic linking path. >
Well I added -I/usr/local/vmd/plugins/include to CPPFLAGS and -L/usr/local/vmd/plugins/FREEBSDAMD64/molfile to LDFLAGS and the recompiled editconf is still uable to properly parse the vmd-style pdb Oh well -- ================================================================== 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
