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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