AMBER Archive (2003)

Subject: Re: mm_pbsa nmode calculation

From: kbyun_at_wesleyan.edu
Date: Wed Apr 23 2003 - 15:33:55 CDT

Hi,

I generated the restart file in the directory

~/Examples/04_MMPBSA_Nmode

with the command

mm_pbsa.pl mm_pbsa.in

using the default .in file and perl script in amber7

Our machine is a pc cluster that uses red-hat linux.

Thanks,

Suzie

> Dear Suzie,
>
> kbyun_at_wesleyan.edu wrote:
> >
> > Hi,
> >
> > I'm running the tutorial for mm_pbsa and I have two
> > question about the nmode calculation.
> >
> > First - the restart file generated by mm_pbsa.pl -
> > sanmin_lig.1.restrt for the calculation is not
human-
> > readable. How can I get one that contains the
typical
> > format?
>
> Actually - I don't see at the moment how you could get
> non-human-readable files with the combination of
mm_pbsa.pl and
> make_crd_hg of AMBER 7. Would you describe how you
generated your
> *.restrt file? On what machine, ...
>
> > Second - I get an error message when mm_pbsa.pl
tries
> > to run nmode with this restart file, I run into
memory
> > problems:
> >
> > Total memory required :
> > 20855890 real words
> >
> > Total memory avail : 3500000 real words
> >
> > Total memory required : 80201 integer words
> >
> > Total memory avail : 4000000 integer words
> >
> > Maximum nonbond pairs 3919798
> > increase the real memory by 17355890 words
> >
> > I thought amber programs were compiled to run
systems
> > of 30,000 atoms or so. The system in this tutorial
has
> > ~3000. Do I need to recompile nmode or can this
have
> > something to do with the restart file?
>
> Normal mode analysis is pretty memory-demanding (see
related postings on
> the amber list for this), that's why nmode is not
compiled by default
> for such a number of atoms. So you need to recompile
nmode.
>
> > Thanks!!
> >
> > Suzie Byun
>
> Best regards
>
> Holger
>
> --
> +++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
> Dept. of Molecular Biology, TPC15
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> La Jolla CA 92037 USA
> phone: +1-858-784-9788
> fax: +1-858-784-8896
> email: gohlke_at_scripps.edu
> +++++++++++++++++++++++++++++++++++++++++++++
>