[gmx-users] Problem about Cgenff lone pairs

Shujie Fan gn8008 at hotmail.com
Sat Feb 9 22:05:47 CET 2019

Thanks for your help.

Best wishes,

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Friday, February 8, 2019 11:58
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem about Cgenff lone pairs

On 2/7/19 4:35 PM, Shujie Fan wrote:
> Dear all,
> I would like to run simulation for some small molecules containing
> Chlorine with CHARMM36 forcefield. I was using cgenff to generate
> the gromacs topologies. It seems cgenff_charmm2gmx.py  script
> currently cannot convert topologies containing lone pairs.
> Does anyone know other way to generate gromacs topologies from str file from cgenff?

Automatic conversion of lone pairs is not yet supported, but we are
testing a script to include this feature. The main problem is that
GROMACS does not (yet) support simple lone pair construction like we
have in CHARMM, so our only current method is to hack a virtual site
construction type, but the way we do it was turned into a fatal error
after GROMACS 2016. When GROMACS can officially support the required
virtual site construction type, we will be able to release a finished
version of the CGenFF conversion script (and we will have versions for
Python2 and Python3).



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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


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