AMBER Archive (2007)

Subject: AMBER: Modified nucleotides-ATOM TYPES

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Mon Feb 26 2007 - 03:13:59 CST

Dear amber users,

I am trying to parametrise a modified nucleotide. The DNA molecule which I am trying to simulate contains normal nucleotides as well as modified ones. When I am assigning AMBER atom types, there are some missing angle parameters. So I tried GAFF, and in this case there are no missing parameters. My question is, Is it a reasonable approach to use amber atom type and gaff atom type for the same molecule? If not how can I assign missing parameters for amber atom types?

Thanking you,

Mathew

                                 
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