[gmx-users] OPLS3 forcefield

[Krzysztof Kolman]

I use and recommend the project STaGE (OPLS-AA and other forcefields):

https://gerrit.gromacs.org/#/admin/projects/STaGE

Best regards,
Krzysztof

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!
>
> Alex
>
>
> 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:
>>
>> http://zarbi.chem.yale.edu/ligpargen/oplsaam_gmx_tutorial.html
>>
>> This will generate a pair of itp and gro files with assigned custom OPLS
>> types for the atoms (along with charges).
>>
>> -Micholas
>>
>> ===================
>> 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
>> proceed?
>>
>> Thanks,
>> Neha
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