Do you get the same error for AMBER16?
I think people mostly use MMPBSA.py nowadays.
Hai
On Wed, Feb 8, 2017 at 11:36 PM, wei <lwstudy.sina.com> wrote:
> 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
