Thanks Bill and Jason.
So, Jason, what would be the answer to my original question?
On 4/12/17 10:32 AM, James Kress wrote:
> If I have a reference DNA oligomer like:
>
> CGCGAATTCGCG
>
> And want to do an rmsd against a trajectory of a DNA oiligomer like:
>
> GCGCTTAAGCGC
>
> Will rmsd reorient the reference (or trajectory) so that the sequences are properly compared, i.e. the AATT sequence in the reference is compared to the TTAA sequence in the trajectory where the A's and T's are compared against A's and T's instead of T's being compared to A's?
What commands or parameters do I need to specify to do this?
Thanks.
Jim
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Wednesday, April 12, 2017 2:41 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] reorientation in rmsd
On Wed, Apr 12, 2017 at 2:28 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Unless I've missed a change, RMS can only be performed between
> identical molecules in Amber.
>
>
That change is cpptraj replacing ptraj :). This is no longer a restriction. The original impetus was this problem, IIRC.
All the best,
Jason
--
Jason M. Swails
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Received on Wed Apr 12 2017 - 12:30:02 PDT
