[gmx-users] OPLS3 forcefield
krzysztof.kolman at gmail.com
Wed Apr 11 14:32:15 CEST 2018
I use and recommend the project STaGE (OPLS-AA and other forcefields):
2018-04-07 23:04 GMT+02:00 Alex <nedomacho at gmail.com>:
> Not sure about OPLS3, but for the publicly available OPLS-AA there are
> many resources, because OPLS in general is a bit of LEGO.
> My favorites:
> 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
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users