[gmx-users] oplsaa parametrization

[Ran Friedman]

Hi Rosa,

You can read the paper on PRODRG to study how they parametrise.
There's a topology builder for OPLS-AA:
http://labmm.iq.ufrj.br/mktop/

There're also commercial tools (see some previous posts on the mailing
list) and you can also start with PRODRG and modify the files to have
the right parameters as in GMX.

However, you should verify that your molecules are correctly
parametrised no matter what software you're using - run a simulation
with it and see if things look all right (e.g., if rings are not too
distorted, bonds are correct etc.) and try to get experimental
parameters to compare with.

It has been stressed out a lot in the list that this is an advanced
issue - being familiar with MD and the FF you're using is a
pre-requisite to parametrisation.

Good luck,
Ran.
>
> Dear Ran
>
> Thanks for the reply. I think I `ve read some papers using PRODRG and
> opls. However they didnt mention clearly that how they parametrized
> their force field. Just do you know any alternative software. As I
> checked many softwares but I couldnt find any to create .itp file at
> the same time. Thank you.
>
> Regards
> Rosa
>
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