Hello All,
I would like to calculate the entropy of a protein+RNA system. I use MM_PBSA
script and within it NM parameter (nmode). I also incorporate complex, receptor
and ligand with my calculation. I get the following runtime error from the
script:
=>> Init data
Presuming executables of amber suite to be in
/home/software_linux/depot/amber/amber9/exe
=>> Reading input parameters
Found n => GC).
Found PREFIX => output2_nm
Found PATH => ./output_nm
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => complex_mg.prmtop
Found RECPT => receptor.prmtop
Found LIGPT => rna_mg.prmtop
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 0
Found GB => 0
Found PB => 0
Found MS => 0
Found NM => 1
Found DIELC => 4
Found MAXCYC => 50000
Found DRMS => 0.0001
=>> Checking sanity
Checking GENERAL
Checking NM
=>> Creating input
Nmode input
=>> Calculating energy / entropy contributions
Calc contrib for ./output_nm/output2_nm_com.crd.1
Minimize structure
Calc entropy
Fortran runtime error: Attempt to allocate negative amount of memory. Possible
integer overflow
/home/software_linux/depot/amber/amber9/exe/nmode -O -i nmode_com.in -o
nmode_com.1.out -c sanmin_com.1.restrt -p complex_mg.prmtop not running
properly
Referring to nmode_com.1.out, I see the following memory allocation reported:
*******************************************************
Initiate the NMODE module of AMBER 8
*******************************************************
File generated by mm_pbsa.pl
ntrun maxcyc ibelly drms
1 100 0 0.10E-02
rcut scnb scee dielc idiel
99.00000 2.00000 1.20000 4.00000 0
nsave dfpred bdwnhl smx emx alpha ndiag
20 0.01000 0.10000 0.08000 0.30000 0.80000 10
ipol = 0
i3bod = 0
nvect = 0
Binary format used for input coords.
| New format PARM file being parsed.
| Version = 1.000 Date = 09/15/09 Time = 13:23:58
PARM file has the title:
Total memory required : 453813873 real words
Total memory required : 17167813 integer words
Total memory required : 17707 4-character words
Maximum nonbond pairs 16793909
As can be seen, the system requires a huge memory. I was wondering if anyone
would have a similar experience and can advise me how I tackle memory
management for this calculation.
Thank you,
Alireza
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Received on Tue Oct 06 2009 - 08:30:02 PDT
