From: Maxim Igaev (maxim.igaev_at_Biologie.Uni-Osnabrueck.DE)
Date: Mon May 04 2015 - 06:47:09 CDT
Hi Jerome,
thanks for your reply! This is a good point. The other software can
process different PDB conventions. I don't know which one accepts atom
IDs in hexadecimal format though. But I will try. A hardcore way would
anyway be to maually convert the second column in the PDB file into DEC
with a Python script =)
Regards,
Maxim
> 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/
>
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>
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