Dear Salma,
> i have installed amber sucessively. but its GUI is not being supported
> by my system as some of its applications have GUI. how to get these GUI for
> various tools. i am doing modeling of a ligand that i draw by myself in
> ISIS DRAW tool. when i upload the file of ligand on the amber12 it gets
> struck by giving a message" FATAL: Atom .R<MOL 874>.A<H80 39> does not
> have a type" how i can assign atom types to my ligand molecules.
I might be wrong but using ISIS DRAW will lead to a structure
represented in 2D and consequently to the absence of definition of a
conformation... If so, you generate a bad input structure for geometry
optimization. You could use another program/tool (xLEaP, R.E.D.
Server, etc...) to build your input structure in 3D.
Then, once your input structure is correct you can use a program to
set its atom types, although learning the different atom types and
adding them manually allows better controlling what we do.
regards, Francois
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Received on Tue Jan 08 2013 - 00:30:02 PST
