[gmx-users] x2top strange behaviour

Steven Kirk Steven.Kirk at htu.se
Fri Sep 23 14:21:10 CEST 2005


I have a PDB (with CONECT records) file which I'm running through x2top 
to generate a topology file. This (apparently) works fine - the output 
from x2top mentions that it is finding bonds, and indeed in the output 
topology file, the sections [bonds] and [angles] appear, together with 
listings of which atoms ID numbers are connected to other atom ID 
numbers, etc.

The problem is that these two sections contain fields for c0-c3 
(function coefficients), just after a function field which x2top sets to 
1. In the topology file produced by x2top, no numerical values appear 
for c0-c3 (i.e. the fields are blank).

I know that x2top can generate values in these fields (I have old 
topology files generated for similar data files), but I have forgotten 
what information x2top needs to see in order to 'fill in the gaps'.

I am using the OPLS force field, with some extra defined atom types 
earlier supplied by David, but I can't work out why x2top can't see the 
necessary potential function data.

Presumably this information is extracted from the first file called 
'ffoplsaabon.itp' found, either under the installtion location or the 
current directory ?

Is there any way (command line switch?) to see exactly which files x2top 
is trying to access, or needs to access, to get the full [bonds] and 
[angles] information ?

Many thanks in advance,
Steven Kirk

Dr. Steven R. Kirk          <Steven.Kirk at htu.se, S.R.Kirk at physics.org>
Dept. of Computer Science, TMD               http://taconet.webhop.org
Univ. of Trollhattan/Uddevalla   Ph: +46 520 475318 Fax:+46 520 475399
P.O. Box 957 Trollhattan 461 29 SWEDEN

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