AMBER Archive (2008)

Subject: AMBER: Simulating DNA Backbone in NAB

From: Adelene Sim (adelene_at_Stanford.EDU)
Date: Tue Apr 01 2008 - 14:23:16 CDT

Hi, I'll like to do a MD simulation of just the DNA backbone (i.e. no
side-chains, replace the bases by a H) in NAB. Is it possible to just add in
entries into the force-field library (e.g. all_nucleic94.lib), where I
remove the side chain atoms and replace them by a H atom? (Of course I'll
also change the charges on the atom.)

 

Are there any other files I'll need to modify? I can't seem to get this to
work.

 

Thanks!

 

Adelene

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