AMBER Archive (2006)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Jun 28 2006 - 11:22:42 CDT

> 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 :
>
> traj.in dna.binpos
> pucker res1 :1_at_C1' :1_at_C2' :1_at_C3' :1_at_C4' :1_at_O4' out phaseangle.out time 0.2

Yes, this is what I routinely do...

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