From: Behnam Rasti (b81r60_at_gmail.com)
Date: Wed Sep 25 2013 - 06:20:35 CDT
dear namd users,
i want to calculate the interaction energy for each pair of residues
between a ligand and the binding site of a receptor.
i have used the following command but it gives pair interaction
between ligand and receptor (not residue by residue) in each time
step.
##########################################################
pairInteraction on
pairInteractionFile pair_tmp.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2
set ts 0
coorfile open dcd out/run.dcd
while { ![coorfile read] } {
firstTimestep $ts
run 0
incr ts 1
}
coorfile close
###########################################################
I have been thinking of using the same command several time, each time
putting 1 & 2 in beta column of only one residue of the ligand and
binding site respectively. but it is very time consuming.
I really appreciate if any body has a better idea.
tnx
Beh
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