From: Shirley Siu <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] histidine (HISB) planarity >> how about Trp?
Date: Mon, 14 Aug 2006 18:07:13 +0200
Hi everybody,
I am also trying G53a6 in my protein simulation and it is observed that TRP
is less planar as compared to those in OPLS. The angle distribution of the
impropers are calculated to be wider and thus less populated in the
equilibrium angle. Would this hint to a problem in the setup or ff?
I do not think there is an error in ffG53a6.rtp for TRP.
OPLS and GROMOS use different approaches to keep
rings planar.
I don't know which force field would be closest to reality.
But I think slighlty more or less rigid rings will have little
influence on the properties of proteins.
Berk.
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