Re: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering

From: Thomas Cheatham <>
Date: Wed, 28 Jun 2006 10:22:42 -0600 (Mountain Standard Time)

> What I would like to know is whether or not the following ptraj input
> command is OK to determine the phase angles of ribose sugar residue 1
> taking the dihedral angle about C2'-C3' as the bases and the O4' atom as
> the fifth atom to constitute a pseudorotational angle.
> Here is my ptraj input :
> dna.binpos
> pucker res1 :1.C1' :1.C2' :1.C3' :1.C4' :1.O4' out phaseangle.out time 0.2

Yes, this is what I routinely do...

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Received on Sun Jul 02 2006 - 06:07:07 PDT
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