[AMBER] Binding energy using mm_pbsa.pl

From: Wong, Sook (NIH/NCATS) [V] <"Wong,>
Date: Thu, 6 Nov 2014 16:28:57 +0000

Good morning amber user,

I am trying to obtain binding energy with mm_pbsa.pl using Amber12 (Not sure why Amber14 isn't working for our system). However, when I was trying to extracts the coordinates for complex, ligand and solvent. I received the following:

Argument "1 # number of lig" isn't numeric in numeric lt (<) at /*/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 908.
Argument "1 # number for rec" isn't numeric in numeric lt (<) at /*/amber12/src/mm_pbsa/mm_pbsa_createinput.pm line 925.

Is this the reason why there is an error when trying to compute the free energies using GB models? The log of binding energy came out to have the following:

    Processing GB GBTOT
        Doing 1 GB GBSOL
        Doing 1 MM GAS
    No values for MM_GAS existing -> Skipping
    For details see: http://ambermd.org/Questions/mm_pbsa.html#calc_missing_no_value_skipping
    Processing GB GBELE
        Doing 1 GB GB

Appreciate with your help.

-Sook Wong

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Received on Thu Nov 06 2014 - 08:30:03 PST
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