Dear Amber list experts,
I use a standard cpptraj scipt for the generation of the average 3D structure of
receptor - ligand complex:
parm ../mc.prmtop
trajin ../5_/mc_md3.mdcrd
trajin ../6_/mc_md4.mdcrd
trajin ../7_/mc_md5.mdcrd
trajin ../8_/mc_md6.mdcrd
trajin ../9_/mc_md7.mdcrd
trajin ../10_/mc_md8.mdcrd
strip :WAT
strip :Cl-
center :1-508 mass origin
image origin center familiar
average av_md3-8.pdb PDB
run
quit
My question is: How to modify the cpptraj script in order to collect
for the averaging only that MD frames
where the interatomic distance:
distance R5_E89 :5.67 :89.1503
belongs to the interval from 3 to 5 A?
Many thanks,
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 Mon Feb 15 2016 - 09:00:04 PST
