[gmx-users] pdb files using hex resid

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 4 05:55:35 CET 2012

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.


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