Dear Amber List users,
I now how write a cpptraj script for the generation of average protein structure from
MD simulation in one directory as for instance:
cpptraj
parm ../sm.prmtop
trajin ../3_/sm_md3.mdcrd 1001 2000
strip :WAT
strip :Cl-
rms first .C,CA,N
average average.pdb PDB
run
Unfortunately, I don't know how to write a cpptraj script for time interval
that covers the border between two sequential directories of continuous
MD simulation like in the task described below.
I have ran productive MD simulation of my protein
in two sequential time intervals 20ns (2000 snapshots) in directory 3_,
and then continuing simulation of 20ns (2000 snapshots) in directory 4_.
As a result I have in total 40ns (4000 snapshots) MD simulation.
I want to generate average 3D structure of my protein on the last 30 ns
(3000 snapshots) time interval that includes a border between two
sequential MD simulations.
What should be a cpptraj script for this case?
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Thu Sep 10 2015 - 01:30:03 PDT
