[gmx-users] pdb files using hex resid

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 4 03:21:01 CET 2012

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.

> Is there another tool with which I can do specific selections and write
> them out to something I can reinput into gromacs?

Script g_select?


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