[gmx-users] pdb files using hex resid
Peter C. Lai
pcl at uab.edu
Wed Jan 4 04:19:08 CET 2012
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
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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