Hello, If you want to use CHARMM for your simulations, do not use PRODRUG to construct your parameters but use ParamChem, instead.
https://www.paramchem.org/ Stéphane ------------------------------ Message: 2 Date: Wed, 12 Jul 2017 14:36:27 +0500 From: maria khan <mariabiochemi...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] topology servers versus ff. Message-ID: <caenliddelrz5kj+hotxbvguvvmt9ecwmh4o7qeoljcantnd...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear gromacs users.. while using charmm27 can i use PRODRUG for topology building.?? when im using prodrug pdb2gmx gives me error of missing atoms but when i use charmm ff,it doesnt give me that error,so proceeding with charmm27 i made ligand topology by prodrug and used it for further simulation,when comes to adding ions step it gives me error of ""atomtypes CH3 not found"". thanks. ------------------------------ -- 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. End of gromacs.org_gmx-users Digest, Vol 159, Issue 58 ****************************************************** -- 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.