AMBER Archive (2004)

Subject: AMBER: Atom type with/without POL

From: Jiten (
Date: Thu May 13 2004 - 09:01:38 CDT

Dear Amber users,

If I wish to use organic molecules (for example NADP) not having the
polarizability terms but having atom types defined in parm99.dat, how could
I use it with the proteins for which I want the polarizability terms in my
topology file. When topology file is generated with saveamberparmpol, it
gives the polarizability values of the protein of the atom type defined by
the as zero.

In such case do I need to redefine the atom type of the organic molecules
completely different so that there is no similarilty with the parm99.dat Or
is there any other way to deal with it?

Thanks in advance,


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