It is atom number 2524. Look in the pdb output to see which residue it is
in.
On Jun 2, 2011 7:08 AM, "Praapti Jayaswal" <praapti.gmail.com> wrote:
> 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 - 04:30:03 PDT
