AMBER Archive (2009)

Subject: Re: [AMBER] MM - PBSA problem

From: musa özboyacı (musaozboyaci_at_gmail.com)
Date: Mon Jan 26 2009 - 05:15:13 CST

Dear Jenk,There appears nothing wrong with the output, and it did not give
any error. Indeed. The "ELRAELE" problem was occuring while statistics
calculations. I guess there is something wrong in statistics code and the
same problem does not happen in GB calculations.

Best regards,

Musa

2009/1/25 Cenk (Jenk) Andac <cenk_andac_at_yahoo.com>

> Hi Dave,
>
> "David A. Case" <case_at_biomaps.rutgers.edu> wrote:
>
> Just a extra note here: cutcap, xcap, etc. *are* in the &cntrl namelist
> for sander, but not for pbsa. I don't know which program mm_pbsa is
> calling with this input.
>
> Bottom line: the original error may have a very different origin than
> the one I suggested.
>
> ...dac
>
> Thanks for reminding me about using sander in MMPBSA v10.
> I have MMPBSA versions 8 through 10 installed on my computer and I
> sometimes forget what version goes with what.
>
> So, Musa may want to retry the previous pbsa.in using SANDER v10 as
> follows:
>
> sander -O -i pbsa.in -o pbsa.out -p prmtop -c snapshot1.x
>
> I wonder now how pbsa.out will come out.
>
> cheers,
>
> jenk
>
>
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