[gmx-users] topology servers versus ff

ABEL Stephane Stephane.ABEL at cea.fr
Wed Jul 12 12:12:35 CEST 2017


If you want to use CHARMM for your simulations, do not use PRODRUG to construct your parameters but use ParamChem, instead. 




Message: 2
Date: Wed, 12 Jul 2017 14:36:27 +0500
From: maria khan <mariabiochemist1 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] topology servers versus ff.
        <CAEnLiddELrz5Kj+HoTxBvGUvVmT9eCWMH4O7qEoLJcANtNdcdQ at 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"".



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