Re: [AMBER] FW: Re: How to Calculate SASA with Amber?

From: E. Nihal Korkmaz <enihalkorkmaz.gmail.com>
Date: Sun, 19 Aug 2012 22:49:25 -0500

I am also having the same problem with the following command and input
file, I sincerely appreciate any suggestions.

 $AMBERHOME/exe/sander -O -i calc_sasa.in -p ../prot.top -y input_traj -o
sasa.out -c one_of_the_restart_files

Find SASA
&general
   imin=5,
   keep_files=2,
   verbose=2,
   interval=10,
   strip_mask=":Cl-:Na+:WAT",
&end
&gb
  surften=1,
  igb=5,
  gbsa=2,
  saltcon=0.2,
&end

Best,

Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: korkmaz.wisc.edu
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Received on Sun Aug 19 2012 - 21:00:03 PDT
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