atom ID in VMD and NAMD

From: Maxim Igaev (maxim.igaev_at_Biologie.Uni-Osnabrueck.DE)
Date: Mon May 04 2015 - 03:16:09 CDT


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 Igaev, MSc.

Department of Neurobiology

University of Osnabrueck

Barbarastr. 11

49076 Osnabrueck

Phone: +49 (0)541-969 2863

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