[AMBER] GROMACS to AMBER .top and .pdb conversion using gromber

From: cpimenta <cpimenta.itqb.unl.pt>
Date: Sat, 06 Jul 2019 12:56:44 +0100


I used charmm-gui to assemble a bilayer membrane with charmm36 and ran
the protein/membrane system with water and ions for 100ns using
gromacs-2019.1. I tried using gromber to convert the topology and
structure files to amber format using the processed topology and setting
"topdir" but parmed (Version 3.2.0) returns "Action gromber failed
        ParameterError: Not all angle parameters found"

Is it possible to have parmed printing the cases that lead to the error?

Since the membrane was assebled in charmm-gui, charmm36ff files were
downloaded from MacKerell lab webpage and I was able to run MD,
shouldn't all parameters be in the topology?

Will gromber convert to Amber format (using the same FF) or will it
convert to AmberFF?

Many thanks,

AMBER mailing list
Received on Sat Jul 06 2019 - 05:00:02 PDT
Custom Search