AMBER Archive (2009)

Subject: [AMBER] Nmode "not running properly" problem in MM_PBSA

From: Du Yun (ydu_at_mail.shcnc.ac.cn)
Date: Tue Dec 08 2009 - 19:56:48 CST

Dear All:
I've got a problem when performing an mm_pbsa calculation with nmode. My
system has 10080 atoms and in order to calculate the entropy I made the
following modifications to the mm_pbsa and nmode modules:
1) in file src/nmode/sizes2.h:
change " parameter (maxatom=8000)" to " parameter (maxatom=50000)"
2) in file src/mm_pbsa/molsurf.h:
change "#define MAXAT 10000" to "#define MAXAT 50000"
3) in file src/mm_pbsa/mm_pbsa_calceneent.pm
comment the "unlink $nmodeout;" so that I can get the nmode out file
4) in file src/mm_pbsa/mm_pbsa_createinput.pm:
add "print OUT " cut = 10.0, \n"; " after line 95
add "print OUT " cut = 10.0, ismem = 1,\n ";" after line 114
Then I get the error message of

 /home_soft/home/simm03/program_head/amber9/exe/nmode -O -i nmode_rec.in -o
nmode_rec.1.out -c sanmin_rec.1.restrt -p ../Inactive_eq.top not running
properly

    Then I checked the nmode out file, it reads:

 

          *******************************************************

          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

     10.00000 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 = 10/19/09 Time = 14:35:24

 

    PARM file has the title:

 

 

Total memory required : 457748863 real words

 

Total memory required : 51440135 integer words

 

Total memory required : 30910 4-character words

 

Maximum nonbond pairs 50798159

 

     Duplicated 0 dihedrals

 

     Duplicated 0 dihedrals

 

 Getting coordinates from file with title:

 

 

    Number of non-bonded pairs = 3212192

    Number of H-bonded pairs = 0

 

 

 ***************** ***************** *****************

   step = 0

     F = 0.299559E+04 GRDMAX = 0.398139E+02 GNORM = 0.279335E+01

       E-NONB E-ELE E-HBOND E-BOND

    -0.50593E+04 -0.41340E+04 0.00000E+00 0.33950E+03

       E-ANGLE E-DIHED E-NB14 E-EEL14

     0.13515E+04 0.62183E+04 0.20561E+04 0.22235E+04

       E-POL E-3BOD

     0.00000E+00 0.00000E+00

(the file ends here)

I found other users who also have this problem might have the problems like
"ASSERTion 'ier ==0' failed in nmode.f at line 105" because of no adequate
memories. But I don't have this problem. BTW I can run the example 04 for
nmode in the Example folder successfully with the modified modules. Could
you please help me with this problem? Thanks in advance ~

 

Best wishes,

Yun Du

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