On Mon, May 07, 2012, jit mukherjee wrote:
> Thanks for the promt reply.In the tutorial, It is given that, after
> loading the prep file(created by antechember), it has to be loaded
> into xleap so that the unit corresponding to the prep file is loaded
> in leap. ok, upto this point, I understand. But suppose, I creat a
> prep file using antichember named, say, XXX. Now, I have created
> another unit Named YYY using traditional AMBER force field,i.e.,
> PARM99. Now, I load the XXX unit in leap. Now I want to study the MD
> simulation of the YYY-XXX assembly. XXX is bind to the YYY by only
> non-bonded interaction. ok? So, now how will I proceed further? What
> are the comment etc so that I can combine the two units... Can You
> give me some examples on this particular problem?
You need to source both the leaprc file corresponding to the Amber force
field you want, and the leaprc.gaff. Then create a pdb file with both the
XXX coords and the YYY coords (with a TER card between them). Use loadpdb
to load this, then saveamberparm in the usual way.
Note that ff99 is a very outdated force field; I strongly recommed the use of
more recent Amber force fields.
....dac
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Received on Mon May 07 2012 - 11:00:03 PDT
