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 > > -- > Be Yourself @ mail.com! > Choose From 200+ Email Addresses > Get a *Free* Account at www.mail.com <http://www.mail.com/Product.aspx>! > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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