[gmx-users] pdb files using hex resid

[Peter C. Lai]

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

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Peter C. Lai			| University of Alabama-Birmingham
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