[gmx-users] Charmm36 in Gromacs: missing dihedrals

[Mark Abraham]

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.

Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110525/428861d6/attachment.html>