[gmx-users] pdb files using hex resid

[Peter C. Lai]

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.

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