AMBER Archive (2009)

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

From: Mahmoud A. A. Ibrahim (
Date: Sun Jul 12 2009 - 05:37:37 CDT

Dear Dr. Ross
Thanks so much for your reply. Yes, I have found a problem in my inhibitor structure after minimization, and I am working now to figure out the problem.
But, I have a doubt about some points and need someone to place an emphasis on the correct answer:
* I have a lignad has a negative charged oxygen (for example: CH3O-). I couldn't find an tometype for this charged atom, if I treated it as hydroxyle oxygen, during xleap step. So, what should I do?
* The second point, I am going to model an ion (for example Ca2+) and the Ca2+ is bonuded to four residues (i.e. Ca(Res)4). So, I need to calculate the charge of the system (Ca(Res)4) after optimization . Then, what is the difference between:
i- to define Ca(Res)4 as a non-standard residue
and ii- to define each one of our four Res as non-standard residue and Ca as another residue.
I took forward to hearing from you.
Thanks in advance;
M. Ibrahim

Mahmoud A. A. Ibrahim

Current Address
School of Chemistry, University of Manchester,
Oxford Road, Manchester, M13 9PL, United Kingdom.
               Home Address
    Chemistry Department, Faculty of Science,
              Minia University,
             Minia 61519,Egypt.
      Mobile Phone No.: +20102554083
       Land Phone No.: +20226635916
           Fax No.: +20862342601

--- On Sun, 7/12/09, Ross Walker <> wrote:

From: Ross Walker <>
Subject: Re: [AMBER] problem with the energetics of the system
To: "AMBER Mailing List" <>
Date: Sunday, July 12, 2009, 12:52 AM

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

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

> Dear AMBER
> When I do restrain on my protein residue during heating step it gives me the following error:
> NSTEP = 0TIME(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,
>ntb= 1,
>cut= 12.0,
> /
> Keep Protein and inhibitor fixed with weak restraints
> 10.0
> RES 1 177
> --------
> Also, I decreased my restrain to 5, and I got the same error.
> Any suggestions would welcome;
> Thanks in advacne;
> Sincerely;
> M. Ibrahim
> _______________________________________________
> AMBER mailing list

AMBER mailing list

AMBER mailing list