Dear all, I want to calculate entropy contribution of a relatively huge protein (18574 atoms) binding with it's ligand. I used AMBER14 to perform this computation (AMBER16 was tested as well). The task stopped while calculating the normal mode of the first frame. The error information is: ~/software/amber14/bin/nmode -O -i nmode_com.in -o nmode_com.1.out -c sanmin_com.1.restrt -p ./com_nobox.prmtop not running properly
For details see: http://ambermd.org/Questions/mm_pbsa.html#calc_NM_entropy_not_running_properly
Then I open nmode_com.1.out and see: *******************************************************
Initiate the NMODE module of AMBER 8
*******************************************************
File generated by mm_pbsa.pl
ntrun maxcyc ibelly drms
1 100 0 0.50E+01
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
idecomp = 0
nvect = 0
Binary format used for input coords.
| New format PARM file being parsed.
| Version = 1.000 Date = 01/16/17 Time = 12:55:04 PARM file has the title:
default_nameTotal memory required : -1749912621 real wordsTotal memory required : 175055910 integer wordsTotal memory required : 57116 4-character wordsMaximum nonbond pairs 173752760 Normal mode calculation stopped at this point and no further updates were found. Is this problem caused by the requirement of a huge memory? Have anyone meet this problem before? Looking forward your help. Thanks in advance. Regards,Wei--------------------------------
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Received on Wed Feb 08 2017 - 21:00:03 PST
