Dear All,
I found an old script to grab the total energies of snapshots from
MM-PBSA output(
http://amber.ch.ic.ac.uk/archive/200211/0005.html):
#!/bin/tcsh
sed 's/1-4 /1-4/g' $1 > tmp
awk '/^ [BV1]/ {print gas = gas + $3 + $6 + $9} {gas = 0}' tmp > tmp1
paste -s -d " \n" tmp1 > tmp2
awk '{print $1 + $2 + $3}' tmp2 > ${1}.gas
awk '/surface/ {print 0.00542 * $4 + 0.92}' $1 > ${1}.nonpol
awk '/^ c/ {print 0.59616 * $5}' $1 > ${1}.sol
paste -d '" "' ${1}.gas ${1}.nonpol ${1}.sol > tmp
awk '{print $1 + $2 + $3}' tmp > ${1}.all
I am not sure whether it is appliable to amber9. I tried it and found
that EGB mixes up with the gas energy. The nonpolar and polar parts of
solvation energy may also have changed, I guess. If there are some
better ways, please let me know.
Thanks a lot,
Shaowen
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Received on Wed May 16 2007 - 06:07:37 PDT
