AMBER Archive (2004)

Subject: Re: AMBER: Close contact warnings

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 17 2004 - 12:37:06 CST

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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