[AMBER] Use of parmed to generate modified prmtop file

From: Sruthi Sudhakar via AMBER <amber.ambermd.org>
Date: Sat, 24 Sep 2022 11:38:38 +0530

Dear all,

I have a general query. During the production run of a protein simulation
we have written only atoms 1-400 in the trajectory files. While trying to
visualize or analyze the nc file, the original prmtop does not match the
number of atoms in the production nc file. Therefore we modified the
original prmtop file as the following;

parmed complex.prmtop
strip !(:1-400)
parmout com_modified.prmtop

Could anyone please comment if this methodology is fine? or do we have to
follow some other method in this case?

Sruthi Sudhakar
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Received on Fri Sep 23 2022 - 23:30:03 PDT
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