Do you mean, "use pair interactions"? If you're referring to the [ pairs ] section of your topology, well, you will probably need to look at details on the force field to see what it expects, as the answer to this is force field dependent, and I don't typically use OPLS-AA. The [ pairs ] section is usually used to modify 1-4 interactions, but can also be used to modify other interactions if you do things right. This is explained in the manual.
In terms of generating ligand topologies, there are some programs which can do this automatically for OPLS, I think. Schrodinger has one, I believe. Unless you are very well versed in the force field it might be worthwhile looking into this, as obviously, if you make any mistakes in generating your own topology, your results can be garbage. If you are not committed to the OPLS force field, it is also relatively straightforward to automatically generate ligand topologies using AMBER's GAFF force field. Or prodrg can generate topologies for some other force fields. If you are intent on doing it by hand, be sure you know what you are doing, and be very careful. David On 5/28/06, 4tejender <[EMAIL PROTECTED]> wrote:
Dear Gromacs users, I am tring to bulid ligand topology using OPLSAA forcefield. I want to know that should i user pair interactions in the ligand topology. If yes what is criteria for chosing atom pairs for pair interactions with thanks teje _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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