On Tue, Apr 24, 2018, Midhun K Madhu wrote:
>
> Is there a standard procedure which describes how to use Charmm36 modified
> force field in Amber?
What you described below is the standard approach; another is to prepare
Charmm files (psf, ec.), and convert them yourself using parmed. The
two approaches should give the same results, but might provide different
levels of error reporting.
>
> I prepared the prmtop and inpcrd input files using Charmm-gui. They are
> basically converting Charmm input files to Amber input files using parmed.
> How can I make sure all of the non-bonding parameters (LJ parameters) in
> the resulted prmtop file are matching with that in forcefield files?
You can use parmed to examine LJ parameters in your resulting prmtop
file, and compare these manually to what you think they should be.
Comparing all the parameters in anything but a simple system would
probably require writing a script to automate the comparisons.
A simpler test would be to compare LJ energies (for the same
coordinates) in CHARMM and Amber.
...good luck....dac
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Received on Tue Apr 24 2018 - 05:30:03 PDT
