[AMBER] atom charge from MD trajectory

From: King Wu via AMBER <amber.ambermd.org>
Date: Wed, 20 Jul 2022 15:44:38 -0700


I am curious, is there any analysis tool from cpptraj or other softwares to
calculate atom charge from a MD traj? I have the MD traj in either dcd or
pdb format.

Say I want to know the atom charge in frame 1 and the atom charge in frame
2? But then I go back to the fundamental theory in AMBER, the ES energy
term, as well as the prmtop file having all the information about atom
types, charge, bond, dihedral. Then I am thinking since the atom charge is
the same, stored in the protop file, it wont allow one to calculate
individual atom charge in each frame, but people can post-processing using
MMPBSA to get ES energy.

Please advise if I am right or wrong?
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Received on Thu Aug 04 2022 - 13:35:14 PDT
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