AMBER Archive (2007)

Subject: Re: AMBER: sander core dumped during minimization

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 21 2007 - 00:16:11 CDT

On Thu, Jun 21, 2007, zgleo wrote:

> I'm running a conventional MD simulation on a protein with phosphorylated
> residue, using sander.MPI in AMBER9. When I was minimizing the solvated
> structure, the simulation underwent an unusual increase in 1-4 ELE, and
> then core dumped. I wonder how this could take place, and how I could
> solve the problem. Thanks!
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 120 -9.5927E+07 4.0103E+11 8.6740E+13 H1P 2919
>
> BOND = 9090.1760 ANGLE = 688.6095 DIHED = 2952.2263
> VDWAALS = 16630.2146 EEL = -182201.1876 HBOND = 0.0000
> 1-4 VDW = 1096.0431 1-4 EEL = ************* RESTRAINT = 18.5857
> EAMBER = *************

How did you generate the force field for the phosphorylated residue? Look
at the final structure visually: my guess is that there is a proton sitting
right on top of one of the phosphate oxygens. Just a guess, but this behavior
is reasonably common with phosphorylated residues. This hydrogen is probably
atom 2919, so be sure to examine what is going on in its vicinity.

...dac

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