Re: [AMBER] energies too high

From: David A Case <>
Date: Fri, 16 Jan 2015 07:45:31 -0500

On Thu, Jan 15, 2015, Anupam Goel wrote:
> I am new MD/AMBER learner. I am trying to simulate a peptide with
> non-standard residue (PTM). In order to set up files, I am using the
> atomtypes as listed in Cornell et al. On running the MD, the energies go
> really high to 8E10 or indicate NaN. I am having a hard time to figure
> out what is causing this behaviour. If you could help me, please give
> your suggestions on things I could try. The files are attached.

You have close contacts in your struture. If you load the prmtop and inpcrd
files into cpptraj, and type "checkoverlap" and then "go", you will see this:

1 Warning: Atoms 15:LYS_1.HD3 and 27:LEU_2.H are close (0.63)
1 Warning: Atoms 22:LYS_1.HZ3 and 44:LEU_2.O are close (0.60)

If you haven't done so (it's not clear) you need to minimize the structure
before running molecular dynamics. In most cases, bad contacts like this are
easily fixed by a few hundred steps of minimization.

...good luck....dac

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Received on Fri Jan 16 2015 - 05:00:02 PST
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