On 25/05/11, Jon Fuller <jonathan.ful...@gmail.com> wrote: > Dear all, > > I thought that I would reply to this thread as I am having similar > problems and there didn't seem to be an obvious solution. > I wanted to run a simulation of a POPE bilayer using the Charmm36 > parameters from the Gromacs website. So I used pdb2gmx to generate a > .top file. > > I used the input file from this website: > wget http://terpconnect.umd.edu/~jbklauda/research/download/pope80-c36npt.pdb > > pdb2gmx -f pope80-c36npt.pdb -o pope.pdb -p pope.top -ff charmm36 > (I then selected option 3 (tips3p charmm water)) > > I found that whilst pdb2gmx completes 'successfully', no bond, angle > or dihedral terms are generated in the resulting top file. >
I don't understand what you think the problem is. The .top file from which you included excerpts clearly has sections for such terms, and the pdb2gmx output reports generating such. Mark
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