AMBER Archive (2008)

Subject: Re: AMBER: Sander crashes >99999 atoms

From: David A. Case (case_at_scripps.edu)
Date: Fri Jun 13 2008 - 11:59:32 CDT

On Thu, Jun 12, 2008, plmallip_at_mail.uh.edu wrote:
>
> I got .out file, the last lines are:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 70 -2.8473E+04 2.9235E+02 1.1773E+05 SG 5704
> BOND = 213801.9515 ANGLE = 7045.5244 DIHED = 9929.7416
> VDWAALS = 61906.9355 EEL = -375745.2216 HBOND = 0.0000
> 1-4 VDW = 7253.1165 1-4 EEL = 47335.0552 RESTRAINT = 0.0000
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 75 1.3756E+11 1.2563E+10 3.7524E+12 SG 16034
> BOND = 90981.4516 ANGLE = 8650.2958 DIHED = 10103.7688
> VDWAALS = ************* EEL = -388139.7525 HBOND = 0.0000
> 1-4 VDW = 26843.2678 1-4 EEL = 47112.3776 RESTRAINT = 0.0000
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 80 1.3716E+11 1.2523E+10 3.7405E+12 SG 16034
> BOND = 90981.4963 ANGLE = 8650.2956 DIHED = 10103.7688
> VDWAALS = ************* EEL = -388139.7508 HBOND = 0.0000
> 1-4 VDW = 26843.2678 1-4 EEL = 47112.3775 RESTRAINT = 0.0000
> mdinfo file has:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 80 1.3716E+11 1.2523E+10 3.7405E+12 SG 16034
> BOND = 90981.4963 ANGLE = 8650.2956 DIHED = 10103.7688
> VDWAALS = ************* EEL = -388139.7508 HBOND = 0.0000
> 1-4 VDW = 26843.2678 1-4 EEL = 47112.3775 RESTRAINT = 0.0000

The "****" in the VDWAALS lines indicates that two atoms are collapsing on top
of each other (or something similar). Note that the energy changes from
-28,000 on step 70 to 10^11 kcal/mol on step 75. But even on step 70 you
have a bond energy of 213,000 kcal, which is way out of line. You probably
should check you starting coordinates very carefully, and run a few steps of
minimization with ntpr=1 to study things.

Note also that the biggest problems at the above steps are at SG atoms 5704
and 16034. Are you sure that you set up the disulfide bonds correctly in your
protein? Note that you need to add such bonds by hand in most cases.

...good luck...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu