[gmx-users] OPLS3 forcefield
nedomacho at gmail.com
Sat Apr 7 23:04:07 CEST 2018
Not sure about OPLS3, but for the publicly available OPLS-AA there are
many resources, because OPLS in general is a bit of LEGO.
1. http://www.aribeiro.net.br/mktop/ -- sets all atomic charges to zero,
unless you supply a list of manually selected charges. You can get
charges from GMX's ffnonbonded.itp, once mktop has set all the atomtypes
after the first time it was used on your coordinates. You can definitely
make charge lookup automatic, but it is my understanding that the
authors deliberately make the user pay attention to charges.
2. http://erg.biophys.msu.ru/tpp/ -- a pretty intelligent topology
generator. Fails on cannabinoids!
On 4/7/2018 2:37 PM, Smith, Micholas D. wrote:
> As far as I know, OPLS3 is a commercial force-field only for Desmond (not in gromacs). Jorgensen does have an opls/aa/m (I believe that is the name) topology generator on his webpage:
> This will generate a pair of itp and gro files with assigned custom OPLS types for the atoms (along with charges).
> Micholas Dean Smith, PhD. MRSC
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Neha Gupta <nehaphysics17 at gmail.com>
> Sent: Saturday, April 07, 2018 9:36 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] OPLS3 forcefield
> Hi gromacs users,
> How to generate OPLS3 force field parameters for an organic molecule?
> I want to build an automated topology file using OPLS3 force field. How to
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