[gmx-users] pdb files using hex resid

Peter C. Lai pcl at uab.edu
Wed Jan 4 03:07:40 CET 2012

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
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