AMBER Archive (2003)

Subject: mm_pbsa nmode calculation

From: kbyun_at_wesleyan.edu
Date: Wed Apr 23 2003 - 13:33:17 CDT

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?

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?

Thanks!!

Suzie Byun