[gmx-users] Not enough memory. Failed to calloc :

[Justin Lemkul]

On 1/21/16 5:50 AM, Nikhil Maroli wrote:
> Dear all,
> i was trying run g_mmpbsa for trajectory of 100ns protein-ligand system
> with a total of 60686 atoms including water,ions and proteins,
> it ended up with the following error
>
> Fatal error:
> Not enough memory. Failed to calloc -1082130432 elements of size 4 for
> grps[j].nm_ind
> (called from file
> /home/rajendra/software/gromacs_source/gromacs-5.0.5/src/gromacs/fileio/tpxio.c,
> line 2510)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Kindly advice me the on this problem
>

Water and ions should not be part of an MM/PBSA calculation.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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