yes, that is what I had meant. It may well be that they are entirely the
same, but I've found the error messages from the python one to be more or
less understandable.
On Thu, Nov 6, 2014 at 3:05 PM, Wong, Sook (NIH/NCATS) [V] <
sook.wong.nih.gov> wrote:
> Hi Aron,
>
> The python version is it using the MMPBSA.py method?
>
> -Sook
>
> -----Original Message-----
> From: Aron Broom [mailto:broomsday.gmail.com]
> Sent: Thursday, November 06, 2014 2:52 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Binding energy using mm_pbsa.pl
>
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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>
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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 - 12:30:03 PST
