Dear Bill,
The problem is fixed now. Thank you very much.
Best wishes
Phuc
2011/9/14 Bill Miller III <brmilleriii.gmail.com>
> 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
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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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Received on Thu Sep 15 2011 - 20:30:02 PDT
