Re: [AMBER] Error while umbrella sampling with distance restraint

From: Jason Swails <>
Date: Fri, 26 Jul 2013 08:15:20 -0400

On Thu, Jul 25, 2013 at 2:45 PM, Meekyum Olivia Kim <>wrote:

> Hello,
> I'm trying to do umbrella sampling in implicit solvent with distance
> restraint to calculate the PMF while pulling out the ligand from the
> protein. I'm doing minimization with the adjusted distance between the
> ligand and the receptor center of mass defined in the restraint file,
> without SHAKE, then followed by two equilibration with SHAKE turned on. The
> first equilibration fixes the protein with a small force constant. But the
> first equilibration didn't start and I got this error message regardless of
> the distance between the ligand and protein:
> | ERROR: I could not understand line 190
> 13.2773028 9.5137563 26.5189041************ 404.8478369************
> *s in the inpcrd file often indicate an overflow of the Fortran format used
> to store coordinates in the inpcrd/restart files. This often happens when
> particles diffuse very far away from each other. Make sure you are removing
> center-of-mass translation (nscm /= 0) or check if you have multiple,
> mobile
> molecules that have diffused very far away from each other. This condition
> is
> highly unusual for non-periodic simulations.

This is a very detailed error message that gives you several possible
explanations about why this error occurred. In fact, I wrote this error
message based on replies that you would typically get if you asked about
the cryptic error message "Error during floating point read" on this list.

GB simulations should NOT have multiple molecules, unless they are
non-covalently bound. Otherwise this error will occur with a long enough

I second Levi's suggestion that you should visualize your system.
 Visualization often yields good clues about what went wrong.

Good luck,

P.S. Please wait at least a couple days before reposting your question.
People will respond as they have time (and it may take a couple days for a
knowledgeable person to get to your question).

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 26 2013 - 05:30:07 PDT
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