jalemkul at vt.edu
Wed Sep 12 14:16:50 CEST 2018
On 9/12/18 4:19 AM, Frederic Schneider wrote:
> 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.
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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