AMBER Archive (2004)

Subject: Re: AMBER: MD problem.

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 17 2004 - 10:36:04 CST

On Wed, Mar 17, 2004, Osman Gani wrote:
>
> I have been using AMBER 7 on HP SuperDome. I am trying to run MD of a
> LIGAND+PROTEIN complex. With other ligands, everything went well with the
> same PROTEIN. I guess, I am having problem in parameterization of my current
> LIGAND. I used PARMCHK in ANTECHAMBER (always using "-at amber") to get the
> parameters.In the " ATTN, need revision" space , I manually added some
> parameters in accordance with PARM99.dat.Initial minimization was ok. But MD
> stopped with error message-
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 6 4 4055 4054

Are you sure the initial minimization was OK? Usually when you get shake
failures right at the beginning, there is something wrong with the energies.

Try the usual advice: run a short simulation with ntpr=1. That way you
can see a lot more about what is happening.

...good luck...dac 

-- 

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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
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