did you try the python version of AMBER14? I don't know how much they
differ, but I feel like the python one may have more users at the moment.
On Thu, Nov 6, 2014 at 11:28 AM, Wong, Sook (NIH/NCATS) [V] <
sook.wong.nih.gov> wrote:
> 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:
>
> skipping
> 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.
>
> Sincerely,
> -Sook Wong
>
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Nov 06 2014 - 12:00:03 PST
