AMBER Archive (2007)

Subject: Re: AMBER: NAB Average Structure

From: adelene_at_Stanford.EDU
Date: Thu May 17 2007 - 13:59:42 CDT

Thank you. Is there "ptraj" feature in NAB? I don't see that in the manual.

I was thinking more in terms of combining different pdb output files
which I obtained from MD in NAB - is there a way of averaging out the
structures? I'm also concerned if this will cause unphysical bond
angles and lengths, so any advice is welcome.

Adelene

Quoting "David A. Case" <case_at_scripps.edu>:

> On Thu, May 17, 2007, adelene_at_stanford.edu wrote:
>
>> Hi, is there a way to use NAB to generate the average coordinates of
>> stuctures simulated using MD?
>
> You could save the trajectory (comes out in "binpos" format, I think), and
> then use ptraj to compute the structural averages.
>
> Otherwise, the idea behind NAB is that you could modify the code internally.
> But remember that you probably want to remove overall translation
> and rotation
> before computing the average structure, so the ptraj route (where all that
> stuff is already worked out), may be the way to go.
>
> ....dac
>
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