[gmx-users] Charmm36 in Gromacs: missing dihedrals
mark.abraham at anu.edu.au
Wed May 25 14:19:59 CEST 2011
On 25/05/11, Jon Fuller <jonathan.fuller at 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.
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