How to set improper dihedral for trans-double bond.

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Mon Nov 29 2010 - 06:15:16 CST

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Dear all,

I am trying to set an improper for a trans-double bond. In the attached pdb
file, I am trying to set
an improper for the NH1=NH1 double bond. It seems that the improper "CD
NH1 CD NH1"
with angle value set as "0.00" always leads to unstable simulations, and the
NH1=NH1 double
bond always goes to the cis-configuration.

I appreciate a lot for your help.

Boyang.

-- 
Boyang Wang, Ph.D.

• chemical/x-pdb attachment: trans.pdb

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