AMBER Archive (2002)

Subject: BondEn shoots in solvent minimization

From: suvendu lomash (suvendu_lomash_at_yahoo.com)
Date: Mon Sep 30 2002 - 10:50:39 CDT

Hi !!
Its me again. I am trying build a protein model using
a crystal structure as template. Since the strucutre
itself had some bad contacts and forbidden torions, I
decided to minimize it first. I now encounter two
problems. First, during minimization in vacuum all
values come down except for that of 1-4 EEl which
stays around 2000 (even though EEl is -2000). Is that
O.K. for a crystal structure? Second, when I take the
vacuum minimized protein and solvate the system,
minimization causes the bond energy to shoots up from
about 30 to 6000. I have tried constraining the
protein molecule and minimise only the water molecules
but with the same result. I have also tried increasing
the box size manually by 0.5A (as suggested to a
similar problem in LINMIN failure section of AMBER
FAQ's) without success. Can you please provide a
physical insight as to why this might be happening and
what the program is actually trying to do?
Thanks
Suvendu.

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