From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon May 04 2015 - 04:52:06 CDT
Hi Maxim,
There is no standard way to handle indices beyond 99999, so I don't think
VMD implements anything else. The whole format is based on constant field
widths though, so increasing one of them seems likely to break everything.
You probably need to either use a different file format, or find out the
convention that your other software uses for large PDB files, and manually
convert PDB files to follow that convention.
Cheers,
Jerome
On 4 May 2015 at 10:16, Maxim Igaev <maxim.igaev_at_biologie.uni-osnabrueck.de>
wrote:
> Hi,
>
> I have a question concerning atom IDs (the second column in a PDB
> file). After generating the pdb/psf pair for a big molecular structure
> in VMD and visually inspecting the PDB file, I noticed that starting
> with atom ID 99999 the numbering switches from DEC to HEX, i.e. after
> 99999 comes 186a0. So this part of PDB looks like this:
>
> ..
> ATOM 99997 CD1 LEU A 428 ...
> ATOM 99998 HD11 LEU A 428 ...
> ATOM 99999 HD12 LEU A 428 ...
> ATOM 186a0 HD13 LEU A 428 ...
> ATOM 186a1 CD2 LEU A 428 ...
> ATOM 186a2 HD21 LEU A 428 ...
> ..
>
> I know, this is probably meant to keep colums in PDB properly aligned.
> The problem is that I need to use the same PDB for simulations with
> another package, and this package cannot read such a PDB in, giving a
> runtime error like
>
> line 4750 in readpdb.f90:
> Bad value during integer read
>
> Does anyone know whether there is a way to tell VMD to not switch to
> HEX after 99999?
>
> Thanks in advance!
>
> Maxim
>
>
>
> ____________________________
>
> Maxim Igaev, MSc.
>
> Department of Neurobiology
>
> University of Osnabrueck
>
> Barbarastr. 11
>
> 49076 Osnabrueck
>
> http://www.neurobiologie.uni-osnabrueck.de/
>
> Phone: +49 (0)541-969 2863
>
>
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