The nmstartframe, nmendframe, and nminterval variables should correspond to
the trajectory made by MMPBSA using the startframe, endframe, and interval
variables in the &general section, not the original trajectory. Thus, you
are trying to take frames 450-500 of a trajectory that only has frames 1-50.
Try changing nmstartframe to 0, nmendframe to 50, and nminterval to 2 and
see if that fixes the problem.
-Bill
On Wed, Sep 14, 2011 at 5:50 AM, hongphuc nguyen
<phucnguyen20072.gmail.com>wrote:
> Dear Amber users,
>
> I have been trying to calculate free binding energy of my system. However,
> there is an error as follows that I don't know how to solve
>
> This is the output file
> | Run on Wed Sep 14 15:57:36 ICT 2011
>
> |Input file:
> |--------------------------------------------------------------
> |mmpbsa
> |&general
> | startframe=450, endframe=500, verbose=1,
> | #entropy=1,
> |/
> |&pb
> | istrng=0.100,
> |/
> |&nmode
> |nmstartframe=450, nmendframe=500, nminterval=2,
> |maxcyc=50000, drms=0.4,
> |/
> |--------------------------------------------------------------
> |Solvated complex topology file: topol/complex.prmtop
> |Complex topology file: topol/com.prmtop
> |Receptor topology file: topol/rec.prmtop
> |Ligand topology file: topol/ligand.prmtop
> |Initial mdcrd(s): prod2.mdcrd
> |
> |Best guess for receptor mask: ":1-269"
> |Best guess for ligand mask: ":270"
> |Ligand residue name is "SUS"
> |
> |Calculations performed using 51 frames.
> |NMODE calculations performed using -198 frames.
> |Poisson Boltzmann calculations performed using internal PBSA solver in
> sander.
> |
> |All units are reported in kcal/mole.
> |All entropy results have units kcal/mole (Temperature is 298.15 K).
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> WARNINGS:
> RADIUS_SET cannot be found in your prmtop files!
> Error in computing entropy! Check nmode output files!
>
> My mdcrd file contains 500 frames. Startframe of nmode is 450 and endframe
> is 500. then the number of frames in nmode is supposed to be around 25 but
> according to the output "NMODE calculations performed using -198 frames". I
> do not understand at what step the error came from
> And will the radius_set effect my results or not?
> Thank you very much
> --
> Thank you very much
> I am looking forward to hearing from you
> Best wishes,
>
> Nguyen Ngoc Hong Phuc
>
> Email: phucnguyen20072.gmail.com
> Mobile phone: +84 984620799
> _______________________________________________
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> 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 Wed Sep 14 2011 - 04:30:04 PDT
