AMBER Archive (2007)

Subject: Re: AMBER: deeper problem with the energetics

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon May 21 2007 - 09:11:58 CDT

I can't really give specific suggestions, other than to try without the
modified parameters (no ligand perhaps)
and see if you have trouble. It could be that some of your atoms don't have
sufficient vdw radii.
you might try searching the archives for more help, this seems to be a
fairly common problem
when people develop their own parameters.

On 5/17/07, Pankaj R. Daga <pdaga_at_olemiss.edu> wrote:
>
> Hi Carlos
>
> Yes, the protein I am simulating is a complex containing
> protein-ligand-DNA and two Mg ions. I have calculted paramaeters for the
> ligand using bcc charges.
>
> How does that affect the total charge? And I would be thankful to you if
> you could help me solving this problem.
>
> Regards
>
> Pankaj
>
>
> ===================================================================
> If your ship doesn't come in, swim out to it.......Jonathan Winters
> ===================================================================
> Pankaj R. Daga |
> Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
> 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
> University of Mississippi | phone: +1-662-915-1853
> University, MS, 38677-1848 |
> ===================================================================
>
> ----- Original Message -----
> From: Carlos Simmerling
> To: amber_at_scripps.edu
> Sent: Thursday, May 17, 2007 8:56 AM
> Subject: Re: AMBER: deeper problem with the energetics
>
>
> I see your charge sum is not zero- are there any force field parameters
> that
> you added? that can also be a common source of shake failures.
> otherwise it seems reasonable to me.
>
>
> On 5/17/07, Pankaj R. Daga <pdaga_at_olemiss.edu> wrote:
> Hi Amber community,
>
> I am running a MD simulation with one homology model, I have built. For
> doing so, I have carried out four step minimization (Solvent, Hydrogen,
> Side-chain and Full), followed by two step heating (0-100 at constant
> volume, force const 20 and 100-300 at constant pressure, force const 10).
> Finally Three step equilibration each 100 ps at constant pressure with
> decreasing harmonic constraints (1, 0.1, and 0). All the precautions were
> taken to equilibrate the system properly.
>
> When I am running the last equilibration step, I ended up in the error
> saying that SHAKE cannot be accomplished. Here is the error as follows. I
> have searched through the archives, for the similar problem. I found that
> these problems are mostly associated with harmonic constraints. In my case,
> I don't have any. Still I am facing this problem.
>
> Can anybody suggest me, what the problem could be? I am attaching the
> input and output file along with.
>
> Please help.
>
> Regards
>
> Pankaj
>
>
> ===================================================================
> vlimit exceeded for step 32333 ; vmax = 82.6417035434410
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 3211 6561 6562
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> ===================================================================
>
>
>
> ===================================================================
> If your ship doesn't come in, swim out to it.......Jonathan Winters
> ===================================================================
> Pankaj R. Daga |
> Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
> 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
> University of Mississippi | phone: +1-662-915-1853
> University, MS, 38677-1848 |
> ===================================================================
>

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