AMBER Archive (2009)

Subject: Re: [AMBER] problem with the energetics of the system

From: Ross Walker (rosscwalker_at_gmail.com)
Date: Sat Jul 11 2009 - 18:52:42 CDT

Hi Mahmoud

I suspect this a problem with your initial structure more than it is a
problem with the restraints. Have you tried it without the restraints?

Did you minimize properly? Have you checked the structure to make sure
it is reasonable?

I would suggest, as a test, turning off shake, setting dt=0.0005 and
running 500 steps with ntpr=1 and ntwx=1 and then visualizing this. In
this way you should be able to work out where the structural problems
are so you can fix them.

Good luck
Ross

On Jul 11, 2009, at 16:23, "Mahmoud A. A. Ibrahim" <m.ibrahim1982_at_yahoo.com
> wrote:

> Dear AMBER
> When I do restrain on my protein residue during heating step it
> gives me the following error:
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> = 0.0
> Etot = -134725.7151 EKtot = 0.0000 EPtot =
> -134725.7151
> BOND = 85.3347 ANGLE = 432.0654 DIHED
> = 1538.9900
> 1-4 NB = 566.6409 1-4 EEL = 7559.2252 VDWAALS = 22730.5512
> EELEC = -167638.5224 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> Ewald error estimate: 0.9061E-04
>
> ---
> ---
> ---
> ---------------------------------------------------------------------
>
> vlimit exceeded for step 4; vmax = 20.9556
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 1286 2654 2660
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> --------------------------
> This is my input file:
> Heating Step of MMP3 (MMMM): stage-1
> &cntrl
> imin= 0,
> irest=0,
> NTX=1,
> ntb= 1,
> NTPR=500,
> NTWX=500,
> NTWR=500,
> ntr=1,
> Tempi=00.0,
> Temp0=50.0,
> NTT=3,
> gamma_ln=1.0,
> NTC=2,
> NTF=2,
> cut= 12.0,
> nstlim=2500,
> dt=0.002
> /
> Keep Protein and inhibitor fixed with weak restraints
> 10.0
> RES 1 177
> END
> END
> --------
> Also, I decreased my restrain to 5, and I got the same error.
> Any suggestions would welcome;
> Thanks in advacne;
> Sincerely;
> M. Ibrahim
>
>
>
>
>
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