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. 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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