AMBER Archive (2007)

Subject: AMBER: Specific/Non-specific dihedral issue in Amber

From: Narayanan Veeraraghavan (narayanan.veeraraghavan_at_gmail.com)
Date: Mon Jul 09 2007 - 09:30:44 CDT

Hi,
I was looking up the dihedral dump from rdparms and I see that in
addition to specific dihedrals, non-specific dihedrals are also
included. For example: H1-CT-CT-OS as well as X-CT-CT-X

I would have thought that if a specific dihedral is available, the
non-specific dihedrals should be ignored. Could someone tell me how
these dihedrals are selected/excluded in tleap?

I'm using Amber 8 with parm99.dat forcefield.

Thanks,
Narayanan 

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