[gmx-users] x2top strange behaviour

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 23 14:31:13 CEST 2005

On Fri, 2005-09-23 at 14:21 +0200, Steven Kirk wrote:
> Hello,
> 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 ?
x2top -h will tell you to use
x2top -param

> Many thanks in advance,
> Steven Kirk
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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