AMBER Archive (2003)

Subject: Re: mm_pbsa nmode calculation

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Apr 23 2003 - 14:12:51 CDT

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
+++++++++++++++++++++++++++++++++++++++++++++