Dear Amber user,
I am defining improper torsion paramter in .frcmod file to reproduce out of
plane bending. Here is 2 question:
1. Since the four atom defined for improper torsion is not serially bonded,
how did LEAP recognize the atom ? I mean if I want to define improper
torsion: PT CB CA CK, and there are many atoms with atom type CB CA CK. Would
leap recognize those 4 atoms with most short distance? Does it depends
on the VWD radius ?
2. I want to define one improper torsion : PT C5 C2 C8 (atom name), but in
guanine base, C4 & C5 share the same atom type CB. If I define one improper
torsion PT CB CA CK (atom type) in .frcmod file, in fact, the improper
torsion would be applied to two set : PT C5 C2 C8, PT C4 C2 C8 (atom name),
right? If it is, any solution to solve the problem?
Thank you very much!
Chen Chengwen
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Received on Sun Apr 08 2007 - 06:07:04 PDT
