[gmx-users] charmm2gromacs.py

Justin Lemkul jalemkul at vt.edu
Wed Sep 12 14:16:50 CEST 2018

On 9/12/18 4:19 AM, Frederic Schneider wrote:
> Hi,
> i use the parameter generator for organic molecules at paramchem.org 
> and i am very thankful, that it was updated for the use of CGenFF 4.0. 
> Now there is a problem with converting the .str file to gromacs 
> topology files. I think, that the python script hosted  on the 
> homepage of the MacKerell Lab does not support the lone pairs which 
> are included since 4.0.  Does anyone know, if there are a newer 
> version of the script?

The script does not yet deal with lone pairs. You will have to add a 
3fad virtual site directive using the information in the LONEPAIR 
line(s) in the stream file. You will also need to add [exclusions] for 
the lone pair, which are the same as the parent halogen atom (within 3 
bonds) since these are not generated automatically.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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