Thankyou for your reply Hirdesh. I have generated the pdb after running
xleap. There are more than one occurrences of atom NZ in the pdb, how do I
understand what problem this atom might be causing?
Thanks in advance!
Praapti
On Thu, Jun 2, 2011 at 2:12 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> Generate the pdb from the finally prepared parameter and trajectories files
> using ambpdb command usage. Then check the atom *NZ 2524* in detail. I
> guess it is the culprit having something unusual.
>
> Hird esh
>
>
> On Thu, Jun 2, 2011 at 9:31 AM, Praapti Jayaswal <praapti.gmail.com>
> wrote:
>
> > Hi All,
> >
> > I am trying to run energy minimization on a protein structure . when i
> run
> > sander it hangs-up after a few seconds and the minimization output file
> > shows :
> >
> >
> >
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> >
> --------------------------------------------------------------------------------
> >
> > ---------------------------------------------------
> > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > using 5000.0 points per unit in tabled values
> > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> > | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> > ---------------------------------------------------
> > | Local SIZE OF NONBOND LIST = 682125
> > | TOTAL SIZE OF NONBOND LIST = 5264395
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 6.4218E+09 7.2626E+08 1.1426E+11 NZ 2524
> >
> > BOND = 123.8350 ANGLE = 415.5306 DIHED =
> > 2022.1738
> > VDWAALS = ************* EEL = -102078.8972 HBOND =
> > 0.0000
> > 1-4 VDW = 1110.2078 1-4 EEL = 9602.0933 RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 5 2.6812E+09 2.7188E+08 4.2715E+10 NZ 2524
> >
> > BOND = 124.1428 ANGLE = 415.7048 DIHED =
> > 2022.1812
> > VDWAALS = ************* EEL = -102085.9218 HBOND =
> > 0.0000
> > 1-4 VDW = 1110.2274 1-4 EEL = 9602.0919 RESTRAINT =
> > 0.0007
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 10 3.7322E+08 2.5957E+07 3.7425E+09 NZ 2524
> >
> > BOND = 128.7875 ANGLE = 417.6624 DIHED =
> > 2022.2293
> > VDWAALS = ************* EEL = -102100.4695 HBOND =
> > 0.0000
> > 1-4 VDW = 1110.3050 1-4 EEL = 9602.0830 RESTRAINT =
> > 0.0107
> > EAMBER = *************
> >
> >
> > The minimization doesn't run beyond this. Could you please help, I am new
> > to
> > AMBER.
> >
> > Thanks in advance,
> >
> > Praapti
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Jun 02 2011 - 04:30:02 PDT
