[gmx-users] x2top

Marius Retegan marius.s.retegan at gmail.com
Thu Jan 29 13:42:14 CET 2009


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.

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

Thank you
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