Dear AMBER users
Was successful in completing MD simulation for our protein sample. We were also able to run successfully the ras-raf tutorial posted on the amber web site including the calculation of deltaG
However,
after generating the snapshots sucessfully, for calculating the binding
energy for our protein sample , the mm_pbsa.pl perl script is showingan error whihc is shown below
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ramesh.sgiUV:~/1FJ1_noheader_info>mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
/data1/apps/amber/10/intel-mkl-openmpi/exe/sander -O -i sander_com.in
-o sander_com.1.out -c ./snapshot_com.crd.1 -p ./1FJ1_AF.prmtop not
successful
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Also attached is the perl script for binding energy and as well as the log file
request you to kindly guide us in overcoming this problem
With sincere regards
Ramesh K V
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Received on Mon Apr 01 2013 - 03:00:02 PDT
