- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Bill Miller III <brmilleriii.gmail.com>

Date: Wed, 28 Mar 2012 15:05:14 -0400

Have you visualized the trajectory made by MMPBSA.py that is being used for

the nmode calculations? I assume that something with the structure is wrong

given the very high energy you are seeing.

-Bill

On Wed, Mar 28, 2012 at 2:41 PM, manikanthan bhavaraju <

manikanthanbhavaraju.gmail.com> wrote:

*> Dear All,
*

*> I am performing nmode calculations for protein-ligand system using
*

*> the following input file
*

*>
*

*> Input file for running entropy calculations using nmode
*

*> &general
*

*> endframe= 10, keep_files=2,
*

*> /
*

*> &nmode
*

*> nmstartframe=1, nmendframe=10,
*

*> nminterval=5, nmode_igb=1, nmode_istrng=0.1,
*

*> /
*

*>
*

*> The 0 frame of the complex, receptor, and ligand got converged
*

*> properly. But for the 1st frame the complex is starting with a higher
*

*> energy
*

*> iter Total bad vdW elect nonpolar genBorn
*

*> frms
*

*> ff: 0 2042644456039025674220868730880.00 80645056.91
*

*> 2042644456039025674220868730880.00 -6856.79 0.00 -43.08
*

*> 2.86e+31
*

*> ________________________________________________________________
*

*> MIN: It= 0 nfunc= 1 E=
*

*> 2042644456039025674220868730880.00000 ( 2.86e+31)
*

*> CG: It= 2 (999.999)q :-((
*

*> LS: i= 1 lhs_f= -1.2156985e+30 rhs_f= -1.9184706e+26
*

*> lhs_g= 7.2029317e+29 rhs_g= 1.7266235e+30
*

*>
*

*> Which is every unusual and causing problems. Towards the end it is showing
*

*>
*

*> LS: step= 1e+20 it= 2
*

*> MIN: It= 9998 nfunc= 499658 E= nan ( nan)
*

*> CG: It= 50 ( nan)q :-(
*

*> LS: i= 1 lhs_f= nan rhs_f= nan
*

*> lhs_g= nan rhs_g= nan
*

*> LS: i= 2 lhs_f= nan rhs_f= nan
*

*> lhs_g= nan rhs_g= nan
*

*> LS: step= 1e+20 it= 2
*

*> MIN: It= 9999 nfunc= 499710 E= nan ( nan)
*

*> CG: It= 50 ( nan)q :-(
*

*> LS: i= 1 lhs_f= nan rhs_f= nan
*

*> lhs_g= nan rhs_g= nan
*

*> LS: i= 2 lhs_f= nan rhs_f= nan
*

*> lhs_g= nan rhs_g= nan
*

*> LS: step= 1e+20 it= 2
*

*> MIN: It= 10000 nfunc= 499762 E= nan ( nan)
*

*> ----------------------------------------------------------------
*

*> FIN: :-) E= nan ( nan)
*

*>
*

*>
*

*> |----Not minimized properly!----|
*

*> |---- Entropy not Calculated---|
*

*>
*

*> Any help?
*

*>
*

*> Thanks,
*

*> mani
*

*> --
*

*> Manikanthan Bhavaraju
*

*> Graduate Teaching Assistant
*

*> Dept. of Chemistry
*

*> Mississippi State University
*

*> office no : 662-325-4633
*

*> MS -39762
*

*> USA.
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Wed, 28 Mar 2012 15:05:14 -0400

Have you visualized the trajectory made by MMPBSA.py that is being used for

the nmode calculations? I assume that something with the structure is wrong

given the very high energy you are seeing.

-Bill

On Wed, Mar 28, 2012 at 2:41 PM, manikanthan bhavaraju <

manikanthanbhavaraju.gmail.com> wrote:

-- 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/amberReceived on Wed Mar 28 2012 - 12:30:03 PDT

Custom Search