Dear Amber community members,
I tried to calculate the entropy of binding for
Estrogen_Receptor-Raloxifene<
http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/Estrogen_Receptor-Ral.pdb>complex
using the follwoing tutorial.
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm
But I'm getting some strange results and all values in the
FINAL_RESULTS_MMPBSA.dat file are written as -1.0000 and Standarad error of
0.000.
Following is the message that I'm getting at the terminal after the job is
finished.
Please find time and see if you can point to what is going wrong?
Attached: FINAL_RESULTS_MMPBSA.dat and progress.log file
------
[vaibhav.localhost Entropy]$ /home/vaibhav/software/amber10/bin/MMPBSA.py -O
-i mmpbsa_nm.in -o FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp
complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd >
progress.log
Assuming /home/vaibhav/software/amber10/exe/sander is part of
amber9 or amber10. Using old PB input file.
Warning: Not all of your snapshots minimized within tolerable limits for
nmode
------
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Wed Jun 09 2010 - 04:30:12 PDT
