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
work.
...good luck...dac
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Received on Wed May 06 2015 - 08:30:18 PDT
