[gmx-users] pdb files using hex resid

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 4 04:54:28 CET 2012

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.


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