AMBER Archive (2004)

Subject: AMBER: mm_pbsa.pl nmode entropy estimating problem

From: jwfang (jwfang_at_mail.ku.edu)
Date: Wed Sep 22 2004 - 14:30:21 CDT

Dear all,
I use mm_pbsa.pl to evaluate the binding free energy for ligand to a 860 AA
protein (16000 atoms). The problem is I have not been able to get nmode to
estimate entropy work. I have been trying several approaches. The newest
attempt is to use AMBER8. I have a quad Opteron system run on RHAS3 with 16
GB memory. I compiled AMBER8 with pgi compiler. However, I keep getting the
following error when I run nmode:

Total memory required : -1811607622 real words
 
Total memory required : 92789421 integer words
 
Maximum nonbond pairs 91943579
Segmentation fault

I modified sizes2.h and change the parameters to huge numbers (see below).
Nmode was compiled but I still got the same error. Could anybody let me know
what went wrong? Does AMBER8 no longer have sizes.h file which can be found
in AMBER7?
    
#sizes2.h
parameter (memdrv=20000000000)
parameter (maxatom=20000)
parameter (maxint=93000000)
parameter (maxvec=50000)

 
! ----- SET THE LIMITS OF SOME ARRAY BOUNDS -----

 
parameter (maxdih = 550000)
parameter (maxdia = 350000)
parameter (maxinb = 900000)
parameter (maxbon = 260000)
parameter (maxbnh = 200000)

Thanks,
--Jianwen

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