[AMBER] Two questions about Net charge and write frcmod in parmed.py

From: Arun Srikanth <askforarun.gmail.com>
Date: Wed, 17 Sep 2014 21:36:39 -0400

Hello. I have two questions,

First question:

I have calculated the partial charges using am1bcc for the atoms in my
molecule (from antechamber). I generated the topology file from the mol2
file from leap. But when I check the netcharge using parmed.py. It is not

It is showing a value of -0.001 for the molecule. Can this be neglected
during a simulation. I am simulating a bulk system so this charge (-0.001)
scaled by the system size is giving a warning in my simulation.

Second question:

When I use the write Frcmod to see the parameters defined in the topology
file. It shows that the bond coefficients are defined multiple times. For

ca - c3
c3 - ca

both have the same coefficients.

I need unique bond types from write Frcmod. I can write script to get the
unique bond types but is there any other way ?

Any help is appreciated.

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Received on Wed Sep 17 2014 - 19:00:02 PDT
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