Hello<br><br>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:<br>
-------------------------------------------------<br>Can not find forcefield for atom O-2 with 2 bonds<br>Can not find forcefield for atom C-10 with 4 bonds<br>Can not find forcefield for atom O-22 with 2 bonds<br>--------------------------------------------------<br>
<br>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.<br>
<br>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.<br>
<br>Thank you<br>Marius<br><br><br>