[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

Hello,

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,
C├ęsar

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Received on Sat Jul 06 2019 - 05:00:02 PDT
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