Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 2 Nov 2015 08:46:33 -0500

On Mon, Nov 2, 2015 at 7:41 AM, Sivanandam M <sivanandamphd.gmail.com>
wrote:

> Dear Amber users,
> I got the following error, at the time of
> running QM/MM calculation of protein -ligand complex. I dont know what is
> the solution of that problem. the error is.
>
> *Sum of charges from parm topology file = -2.99899913*
> *Assuming uniform neutralizing plasma*
> *Running AMBER/MPI version on 40 nodes*
>
> *| WARNING: The number of processors is not a power of 2*
> *| this may be inefficient on some systems.*
>

‚ÄčNeither of these are errors. The first indicates that your system has a
net charge of basically 3 electrons -- there is probably a slight rounding
issue in the charge assignments of your ligand, leading to the non-integer
charge.

If you are running an explicit solvent calculation, you should probably add
3 sodium ions (or something) to neutralize the charge, but even if you
don't Amber will apply a "neutralizing plasma", as it says in the output.

The second warning is purely one about performance. Amber uses a binary
tree with powers-of-two cores to make communications faster, and a
reduce-scatter when it's not power-of-2. All this output means is that the
code is following the slightly less efficient code path for parallelization.

If you are having trouble running the calculation, you will have to show us
the actual error messages, not these warnings.

HTH,
Jason
‚Äč


>
>
> *please help to run the job.*
>
> --------------------------------------------------------
> M.SIVANANDAM
> Research Scholar
> Department of Physics
> School of Physical Sciences
> Periyar University
> Salem-636 011
> Mobile- 9965582730, 9042066076
> --------------------------------------------------------
>
>
>
>
>
> --
> ---------------------------------------------------------------------
> M.SIVANANDAM
> Research Scholar
> Department of Physics
> School of Physical Sciences
> Periyar University
> Salem- 636 011.
> Mobile- +91 9042066076, 9965582730.
> -----------------------------------------------------------------------
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>



-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 02 2015 - 06:00:08 PST
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