AMBER Archive (2009)

Subject: Re: [AMBER] MM - PBSA problem

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Sun Jan 25 2009 - 14:38:16 CST

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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