I think the answer is not so straightforward. It depends upon a lot of things, but I would say that the parameters derived using QM is better. If you do not have any other options you can still use PRODRG server but even in that case, I find many people using the docked (or bound) conformation of the Ligand molecule to generate the initial parameters, which in my view should not be done. One should generate the parameters using the molecule in its minimum energy conformation instead of bound conformation. I would also suggest you to look at the RED server. Please follow this link https://upjv.q4md-forcefieldtools.org/RED/
Thank you On Mon, Aug 19, 2019 at 3:00 PM Priyanka Singh <prinebul...@gmail.com> wrote: > Hii > I am new to simulations. I want to ask is it ok to use ligand topology > build using PRODRG server if using amber force field for RNA-ligand > simulation. what precautions one should take ends of the RNA molecule. > -- > 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-requ...@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-requ...@gromacs.org.
