Hi,
MMPBSA.py no longer uses the program "*nmode"* to calculate the entropy.
MMPBSA.py now uses a nab script to calculate the entropy which is a lot more
efficient because it minimizes and calculates the entropy in one program
thus alleviating the need to use two programs (sander/nmode). From looking
at your output it appears that sander did not minimize the structure
properly and when nmode attempted to calculate the entropy it failed because
the rms gradient of the coordinates was greater than .01. I would suggest
using a more up to date version of MMPBSA.py by downloading AmberTools 1.5.
On Mon, May 9, 2011 at 2:34 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> Dear Dwight McGee and Amber users,
> Thanks for the response.
> The error does not seem to be of Maxcycle but for RMS and some other
> issue in the receptor_nm.out file, which I did not understand.
> Please also suggest which change I should make in the input to handel
> this problem.
>
> The files are attached for your kind reference.
> The *nm.out files show the following error:
> -------------------
> _MMPBSA_LIgand_nm.out
> ***************** ***************** *****************
> step = 0
> F = 0.374349E+02 GRDMAX = 0.195507E+01 GNORM = 0.428118E+00
> E-NONB E-ELE E-HBOND E-BOND
> -0.65651E+01 0.78323E+01 0.00000E+00 0.14371E+01
> E-ANGLE E-DIHED E-NB14 E-EEL14
> 0.10720E+02 0.30799E+02 0.16629E+02 -0.23418E+02
> E-POL E-3BOD
> 0.00000E+00 0.00000E+00
> Root-mean-square gradient of input coords is 0.4281183951692023
> This is greater than the requested maximum: 0.01
> ------------------------
> ------------------------
> _MMPBSA_receptor_nm.out
> PARM file has the title:
>
>
> Total memory required : 290638717 real words
>
> Total memory required : 11052791 integer words
>
> Total memory required : 14203 4-character words
>
> Maximum nonbond pairs 10753202
> ASSERTion ' ier == 0 ' failed in nmode.f at line 106.
> ------------------------------
>
>
> On 5/9/11, Dwight McGee <dwight.mcgee.gmail.com> wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> 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
>
>
--
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 Mon May 09 2011 - 00:30:02 PDT
