Re: [AMBER] Average structure of production run

From: Liao <>
Date: Wed, 17 Jun 2020 04:02:32 +0800

Yes, it is not hard to obtain the average structure, using cpptraj.
A sample script wth file name will look like this:
#cpptraj -i

parm gasphase.prmtop [1]
parm reference.prmtop [2]

trajin gastrajectory.mdcrd parm [1]

#read in reference
reference reference.rst7 parm [2]
#compute rmsd and align the CA atom of residues 1-100 to the reference crystal structure of the same molecule
#refer to p615 of AMBER 19 manual for atom syntax
rmsd rms1 reference :1-100.CA
average 500ns.aligned.pdb
Just run cpptraj -i
and the generated pdb file will be your average structure

Sender:Sruthi Sudhakar <>
Sent At:2020 Jun. 16 (Tue.) 12:27
Recipient:AMBER Mailing List <>
Subject:[AMBER] Average structure of production run

Hello everyone,
I have run 500ns simulation of a ligand-G Quadruplex system, and now need
to obtain the average structure of the run. Is it possible to obtain one
such structure of this 500ns simulation? Is the input same as the one we
use to obtain the pdb of a particular frame of the simulation?
Thank you

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Received on Tue Jun 16 2020 - 13:30:03 PDT
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