AMBER Archive (2004)

Subject: Re: AMBER: Close contact warnings

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Wed Feb 18 2004 - 04:14:55 CST

I checked the output file carefully and found that from step 388 to 389
something strange happened:

  NSTEP ENERGY RMS GMAX NAME NUMBER
    388 -1.5636E+02 4.2407E+00 1.7222E+01 H54 51

 BOND = 11.7069 ANGLE = 77.0644 DIHED = 51.9480
 VDWAALS = -11.8319 EEL = -312.5510 HBOND = 0.0000
 1-4 VDW = 12.5818 1-4 EEL = 14.7250 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    389 -1.0020E+01 7.7049E+01 4.4229E+02 H54 51

 BOND = 161.0069 ANGLE = 168.0122 DIHED = 51.8140
 VDWAALS = -12.2718 EEL = -303.3282 HBOND = 0.0000
 1-4 VDW = 12.8826 1-4 EEL = -88.1358 RESTRAINT = 0.0000

I ran another 440 steps minimization just before the clash one (step 448). I got
the pdb file from the restrt and prmtop and loaded it to xleap. I found that H54
and O41 become one point, which should be two seperated atoms. This tendency
happened from step 389. I do not know why it happened. Is there any method to
avoid this? Thanks a lot.

Lan

Quoting "David A. Case" <case_at_scripps.edu>:

> On Tue, Feb 17, 2004, L Jin wrote:
> >
> > minimization with sander (Amber7)
> > &cntrl
> > imin = 1, maxcyc = 500, drms = 0.0005, ntb = 0,
> > ntpr = 1, cut = 999., ncyc = 100,
> > &end
>
> Have you looked visually at your molecule? Clearly, something very unusual
> is going on. You converge smoothly to a total energy of around -146 at
> step 329, with an rms gradient that is not too large:
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 329 -1.4583E+02 1.1848E+00 4.6123E+00 C31 42
> >
> > BOND = 4.5116 ANGLE = 48.5651 DIHED =
> 44.7987
> > VDWAALS = -11.6564 EEL = -312.0418 HBOND =
> 0.0000
> > 1-4 VDW = 12.4566 1-4 EEL = 67.5408 RESTRAINT =
> 0.0000
> >
> Then something bad happens by step 445; the energy has risen to 0.6, and
> the rms gradient is up to 49. Note that the bond energy especially is
> now very high:
>
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 445 5.9643E-01 4.9484E+01 3.4419E+02 O41 48
> >
> > BOND = 118.4773 ANGLE = 120.6025 DIHED =
> 53.2918
> > VDWAALS = -12.3050 EEL = -305.5181 HBOND =
> 0.0000
> > 1-4 VDW = 12.2175 1-4 EEL = 13.8304 RESTRAINT =
> 0.0000
> >
>
> After this, things get very bad quickly, with some 1-4 contact getting
> very short:
>
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 446 -2.5247E+03 7.9332E+03 5.2102E+04 O41 48
> >
> > BOND = 119.2712 ANGLE = 146.2262 DIHED =
> 52.5048
> > VDWAALS = -12.2562 EEL = -302.8007 HBOND =
> 0.0000
> > 1-4 VDW = 12.4022 1-4 EEL = -2540.0104 RESTRAINT =
> 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 447 -3.0601E+05 1.0647E+08 8.2860E+08 H54 51
> >
> > BOND = 120.7894 ANGLE = 148.1497 DIHED =
> 52.4627
> > VDWAALS = -12.2550 EEL = -302.7370 HBOND =
> 0.0000
> > 1-4 VDW = 12.4228 1-4 EEL = -306025.0251 RESTRAINT =
> 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 448 -3.1064E+05 1.0972E+08 8.2030E+08 H54 51
> >
> > BOND = 120.7918 ANGLE = 148.1526 DIHED =
> 52.4626
> > VDWAALS = -12.2549 EEL = -302.7369 HBOND =
> 0.0000
> > 1-4 VDW = 12.4228 1-4 EEL = -310660.0186 RESTRAINT =
> 0.0000
>
>
> You need to examine your structure carefully (especially around
> atom H54, or maybe around atom O41). I suspect you have something
> "non-chemical" going on.
>
> ...regards...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
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