Dear Dr. Thomas Steinbrecher
when I use crgmask = '.269,271,273,274,275,553,555,556,557'
or crgmask = ":9.O6,H1,N2,H21,H22 | :18.N4,H41,H42,H5"
The run do completely. But, in result section of the out file, there is
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 = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 6629098
| TOTAL SIZE OF NONBOND LIST = 6629098
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -6.0658E+04 4.7164E+01 5.7176E+03 O2P 633
BOND = 828.8853 ANGLE = 1676.8627 DIHED =
567.8802
VDWAALS = 9050.2413 EEL = -72274.8418 HBOND =
0.0000
1-4 VDW = 1531.6803 1-4 EEL = -2038.6314 RESTRAINT =
0.0000
DV/DL = 234.1334
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -6.8494E+04 1.6083E+01 2.7446E+02 C5' 731
BOND = 348.5114 ANGLE = 556.4084 DIHED =
556.4996
VDWAALS = 5168.3350 EEL = -73272.6611 HBOND =
0.0000
1-4 VDW = 281.4572 1-4 EEL = -2132.3336 RESTRAINT =
0.0000
DV/DL = 240.9048
.... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO
*****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
142 -6.9057E+04 1.4742E+01 1.1582E+02 C2 529
BOND = 106.5714 ANGLE = 426.6361 DIHED =
554.1164
VDWAALS = 4954.6681 EEL = -73236.3748 HBOND =
0.0000
1-4 VDW = 274.3817 1-4 EEL = -2137.4799 RESTRAINT =
0.0000
DV/DL = 242.4953
--------------------------------------------------------------------------------
What is RESTARTED DUE TO LINMIN FAILURE?
Is it serious problem? How to fix it?
On Tue, Feb 7, 2012 at 4:14 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > Thus, since DG and DC are not unique in dna, I useed crgmask =
> > (:9.O6,H1,N2,H21,H22
> > | :18.N4,H41,H42,H5).
>
> on a single line, I assume? Try leaving out the brackets and quoting the
> string.
>
> > Can I use atom number rather than atom name? crgmask =
> > '.269,271,273,274,275,553,555,556,557'. is it true?
>
> that should work as well.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 07 2012 - 05:00:05 PST
