[gmx-users] x2top

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 29 13:55:34 CET 2009

Marius Retegan wrote:
> Hello
> I have a question regarding the different implementation of x2top 
> program in Gromacs versions 3.3.1 and 3.3.3 (I didn't test version 4). 
> While trying to generate a very rough topology for a sugar molecule, 
> when I use x2top version 3.3.3 I get the following error:
> -------------------------------------------------
> Can not find forcefield for atom O-2 with 2 bonds
> Can not find forcefield for atom C-10 with 4 bonds
> Can not find forcefield for atom O-22 with 2 bonds
> --------------------------------------------------
> I guess it has to do with the fact that some bonds are longer (or 
> shorter) than a given threshold. I tried to modify the structure of the 
> sugar molecule, but a similar error appears involving other atoms. I 
> used the OPLSAA force field for this, but I doubt that is related. Also, 
> I tried the PRODRG server, but as far as I know it does not support all 
> atom force fields, only UA.

There is no easy way around this. You probably have to start from prodrg 
and edit manually. It may be better if the structure is correct, and you 
could also try to fiddle with the ffoplsaa.n2t file. Anyway you will 
have to correct the files afterwards.

> Regarding the older version of Gromacs I had no problem in generating 
> the file, so I was curios what I can modify to make this work with the 
> never version. I can provide the pdb file if that can help in solving 
> this problem.
> Thank you
> Marius
> ------------------------------------------------------------------------
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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