On Thu, Sep 8, 2011 at 1:46 PM, Steven Burger <stevenburger.gmail.com>wrote:
> I would like to turn on the 1-2 and 1-3 interactions for one particular
> atom.
>
> The one 1-4 interactions be can scaled easily enough, but how would I do
> this with 1-2 and 1-3 interactions.
>
I think you just have to remove them from the exclusion list in the topology
file, but this will take some study of the topology file format (
http://ambermd.org/formats.html), and care to adjust the arrays properly
while maintaining the proper format. You also need to adjust the POINTER
section accordingly for the changes you made. Whether this approach beats
coding is rather subjective :). There's nothing preventing you from
hardcoding the particular interactions you want to include specific to your
system (which is the easiest but obviously least flexible way of doing it),
but that requires you to learn a little Fortran *and* to parse/understand
the sander or pmemd source code...
HTH,
Jason
> Thanks for your help,
>
> Steven
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 08 2011 - 12:00:04 PDT
