Hi,
>>From you results file
*WARNINGS:
igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi
radii (mbondi)
Not all of your snapshots minimized within tolerable limits for nmode. *
It appears the reason you got those particular results pertaining to the
nmode calculation in your output file is because not all of your snapshots
were properly minimized. I would suggest increasing your maximum number of
cycles. Search through your _MMPBSA*nm.out files to determine where this
error occurred and the message *"Not minimized properly!"* should be printed
in the file. It could also be a memory issue but first start with increasing
the max cycles and rerunning the calculation.
Hope that help..
On Mon, May 9, 2011 at 12:46 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> Dear Amber users,
> I had done MD for 3ns for a protein ligand complex. Using this mdcrd
> file I did MM-PBSA/GBSA along with nmode calculation. I have done
> these calculations using AMBER10 and AMBERTOOLS1.0.
> The PB/GB calculation went fine but there seems to be a problem with
> nmode calculation as all the values listed in
> FINAL_RESULTS_MMPBSA.dat are 1.0000.
> Is this result sensible? If not what has gone wrong and what changes
> do I need to make in my input files so that the result becomes more
> sensible.
> Thanking you in anticipation.
>
> (FINAL_RESULTS_MMPBSA.dat file is attached for your kind reference.)
> --
> 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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>
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Sun May 08 2011 - 22:30:03 PDT
