Ross:
Here is my initial pdb file. Thanks
Xuelin
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Ross Walker
Sent: Thursday, September 13, 2007 9:52 AM
To: amber.scripps.edu
Subject: RE: AMBER: Too big EEL energy in energy minimization. .
Dear Xuelin,
I would start by looking at step 0 not step 200. Here you have a huge
VDW
energy. So large that it doesn't fit in the space provided and so is
printed
as stars. This likely means that you have two atoms sitting on top of
each
other. I would take a careful look at your initial starting structure,
particularly in the region of atom 15050 which has an initial force of
over
10^15 KCal/mol/angstrom on it.
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Wang, Xuelin
> Sent: Thursday, September 13, 2007 07:34
> To: amber.scripps.edu
> Subject: AMBER: Too big EEL energy in energy minimization
>
> Dear Amber users:
>
> I got a problem when I did an energy minimization using sander with
> igb=2. after 200 steps, 1-4 EEL energy is too big (see below
> output). I
> checked the pdb file at the 200 step, it seems that hydrogen
> atom is too
> close to nearby opposite charged atoms. I looked through
> Amber Archive.
> someone have the similar problem as mine. it is probably caused by
> "coulomb singularity". but I didn't find any way to fix it.
> Could Anyone
> who know the answer please let me know?
>
> Thanks
> Xuelin
>
> input for minimization:
>
> &cntrl
> imin = 1,
> maxcyc= 200,
> ncyc = 200,
> ntb = 0,
> igb = 2,
> cut = 10
> /
>
>
> output until 200 step
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 1 2.2320E+14 5.5226E+13 6.1959E+15
> C212 15050
>
> BOND = 7614.5838 ANGLE = 10295.7603 DIHED =
> 7006.8784
> VDWAALS = ************* EEL = -17172.9293 EGB =
> -5767.1696
> 1-4 VDW = 2826.7528 1-4 EEL = -6029.6140 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 50 7.5926E+04 1.1788E+02 1.5699E+04
> C311 11126
>
> BOND = 43183.3868 ANGLE = 16384.4780 DIHED =
> 7211.9227
> VDWAALS = 34584.4697 EEL = -16844.8052 EGB =
> -6150.0674
> 1-4 VDW = 3575.6091 1-4 EEL = -6019.1613 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 100 -8.6078E+03 6.5207E+00 4.3093E+02
> C313 1532
>
> BOND = 3016.2527 ANGLE = 8808.6151 DIHED =
> 6951.3959
> VDWAALS = -999.9839 EEL = -16880.7853 EGB =
> -6252.7447
> 1-4 VDW = 3056.8384 1-4 EEL = -6307.3457 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 150 -2.6681E+06 3.9955E+08 6.2474E+10 H2
> 4038
>
> BOND = 2362.1843 ANGLE = 7920.8575 DIHED =
> 6911.7297
> VDWAALS = -1862.9807 EEL = -16849.7311 EGB =
> -6275.6945
> 1-4 VDW = 2949.4612 1-4 EEL = -2663244.3069 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 200 -5.7480E+07 1.8690E+11 2.9224E+13 H2
> 4038
>
> BOND = 2362.1857 ANGLE = 7920.8598 DIHED =
> 6911.7297
> VDWAALS = -1862.9802 EEL = -16849.7310 EGB =
> -6275.6947
> 1-4 VDW = 2949.4612 1-4 EEL = ************* RESTRAINT =
> 0.0000
> MAXIMUM NUMBER OF F EVALUATION EXCEEDED
>
>
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Received on Sun Sep 16 2007 - 06:07:23 PDT
