AMBER Archive (2007)

Subject: AMBER: How to parameterize frcmod for NA

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Tue Feb 13 2007 - 13:27:59 CST

Dear amber community,

I would like some suggestions on the best way to parameterize angles and
torsions for a new residue that has been created. So far I have been looking at
similar angles and using them with their force constants. My biggest challenge
is in determining torsion/dihedral... mainly b/c I have a hard time
interpretting what they mean.

For example, I created an iso-guanosine residue and need to create a torsion for
the C5-C4-N3-N3H or atom types CB-CB-NA-H. I'm not quite sure how to go about
doing this.

Thanks,
Seth
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