The warning you were given (Warning: Not all of your snapshots minimized
within tolerable limits for nmode) can be a little misleading, and may not
always be the case. You should check the nmode output files (_MMPBSA_*nm.out
files) to find more helpful messages. The information you have provided
isn't sufficient to pinpoint the real source of the error.
-Bill
On Wed, Jun 9, 2010 at 7:24 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Jun 11 2010 - 08:30:03 PDT
