[AMBER] Analysis of CHARMM DNA trajectory using nastruct

From: Geoffrey Gray <gmgray2.mail.usf.edu>
Date: Wed, 4 Jun 2014 11:38:07 -0400

Hello, I am trying to analyze DNA from a trajectory produced using CHARMM
(forcefield as well as program). However, I receive the following error:

Error: Ref Atom [C7 ] not found in NA base [THY ]

This is due to the fact that C7 in the Amber force field is C5M in the
charmm force field.

How can I fix this? I tried playing around with resmap, but this was

My script is

parm dcd/dna.psf
trajin dcd/merged-dna.dcd dcd

nastruct naout na.dat resrange :3-33


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Received on Wed Jun 04 2014 - 09:00:02 PDT
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