AMBER Archive (2007)

Subject: Re: AMBER: deeper problem with the energetics

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Thu May 17 2007 - 11:50:11 CDT

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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