[gmx-users] x2top strange behaviour
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
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,
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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