Re: [AMBER] Nmode analysis calculation problem for Implicit simulation.

From: David A Case <>
Date: Wed, 6 May 2015 11:25:52 -0400

On Wed, May 06, 2015, Bajarang Kumbhar wrote:

> My protein and ligand system contain 870 atoms (protein and ligand) so it
> is might be due to large system.

This is not a large system, and should not cause memory problems for most
machines. You would need something like 16*9*870*870 = 110 Mbytes, which you
are likely to have available on any vaguely modern machine.

> >
> > > allocation failure in vector: nh = 1632725649

This is asking for 8*1632725649 = 13 Gbytes of memory. So I don't
understand how you are getting this error message for a relatively
small number of atoms. You might double check all your inputs. As the
introduction to the MM-PBSA chapter emphasizes, you need to figure out how
to run normal mode calculations "by hand" before throwing your system at
these scripts. To start, don't do anything in parallel; create a small
system and compute its normal modes; then see if your 870 atom system will

...good luck...dac

AMBER mailing list
Received on Wed May 06 2015 - 08:30:18 PDT
Custom Search