On 4/01/2012 2:59 PM, Peter C. Lai wrote:
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
Sure... presumably the VMD stuff is only invoked for file types for
which there is not native support. Note that I suggested using some
other intermediate format, not trying to read the non-standard PDB.
Mark
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