Hi Elif,
That's because you don't have the cntrl name list specified. Change
&general to & cntrl and you should be good. You may also need to add a
space before th &'s and it is better to use / instead of &end. So:
Find SASA
&cntrl
imin=5,
Š Š
/
&gb
surften=1,
Š ...
/
All the best
Ross
On 8/19/12 8:52 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
>
>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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 19 2012 - 21:00:04 PDT
