Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed

From: David Case <>
Date: Mon, 24 Sep 2018 23:11:47 +0000

On Mon, Sep 24, 2018, Aravind Ravichandran wrote:

> Thanks for the reply. I tried both. The error occurs before the first
> energy calculation(Before the first step output was written to the file).
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 24998 49727 49728

If you are getting a SHAKE error before the first energy step, then that
narrows down the problem a lot. Try to continue in this vein: run short
(nstlim=10 or 100) simulations with ntpr=1. Narrow down the problem:
does it happen just with the HMassRepartition prmtop, or with both? Does
it depend on dt (try 0.001, 0.002, 0.004)? Does the energy at the first
step match the final energy at the end of the previous equilibration
runs? Is there anything special about atoms 49727 and 49728?

> Moreover, diff prmtop hmr.prmtop shows many lines of differences.

Are all the differences in the mass section of the prmtop? If not,
there is indeed something wrong, and the first step would be to rerun
the parmed step that created hmr.prmtop (in hopes of finding that it
was perhaps just operator error the first time around).

A general note: this is a sort of problem that is generally hard to
resolve via email. I can't really tell (for example) exactly what kind
of run it was that gave the above output. And if there is "garbage" in
the hmr.prmtop file, then of course all the other questions are moot.


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Received on Mon Sep 24 2018 - 16:30:02 PDT
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