AMBER Archive (2009)

Subject: [AMBER] Problem with memory in nmode analysis

From: Alireza Shaneh (ashaneh_at_bri.nrc.ca)
Date: Tue Oct 06 2009 - 10:23:55 CDT

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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