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
zero.
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
eg
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.
Thanks
Arun
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Received on Wed Sep 17 2014 - 19:00:02 PDT
