AMBER Archive (2005)

Subject: AMBER: minimization

From: blakrose_at_gazeta.pl
Date: Fri Aug 26 2005 - 07:20:25 CDT

Dear Amber Users!

I have docked a ligand into my protein (autodock). Now I have got
lot of complexes to minimize. In some number of complexes
minimization is not doing well. Here is the main problem:

After minimization I get BOND=***** but amber menaged to write the
coordinates. I visualized it. It seems like a huge force make two
atoms bond very large. The bond is even as large as protein. Could
it be my mistake or is it amber making it? I don't know what is
happening.

Please help me.
Thanks in advance!!!

Pawel

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