AMBER Archive (2007)

Subject: Re: AMBER: Getting prmtop and inpcrd

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Oct 29 2007 - 13:26:16 CST

> (Residues lacking connect 0/ connect 1 -
> These don't have chain types marked:
> res total affected
> CTHR 4
> NSER 4

The marking of main chain atoms is just for analysis programs that
use atom connectivity info in the prmtop to e.g. derive backbone
torsions. There is no basis for marking the chain for terminal
residues since they don't connect out of 1 end. Unless you are
planning to do this sort of analysis, there is no problem w/ the
above msg.

Bill
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