On Sun, Aug 19, 2012 at 11:52 PM, E. Nihal Korkmaz
<enihalkorkmaz.gmail.com>wrote:
> I am also having the same problem with the following command and input file
> with an error message of the typical " Could not find cntrl namelist", 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
>
You appear to be trying to mix MMPBSA.py input files and sander input
files. I suggest scanning through Chapter 2 of the Amber reference manual
and potentially running through some tutorials on using Amber.
However, if all you're interested in is calculating the surface area of a
trajectory, I suggest looking into cpptraj, specifically the "surf"
command, which can do this.
HTH,
Jason
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Aug 19 2012 - 21:00:04 PDT
