AMBER Archive (2005)

Subject: Re: AMBER: Coordinate Superimposition in PTRAJ

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sun Jan 16 2005 - 08:56:30 CST

if I understand correcly, you want to do a best-fit of two differenr
systems. that can't be done in ptraj - it only allows a single prmtop
and all coordinates used in a ptraj run must match. that means that you'd
have to strip the waters from the reference coordinate too. you'd also
have to leave out the ligand. if that's what you want, you could use a
first
to strip the parts that don't match, and then a second one to fit them.
is that what you had in mind?

Vineet Pande wrote:

> Dear Scientists:
> I want to superimpose a number of 'different' complexes of the 'same
> protein' with different ligands obtained after a PME/PBC MD protocol,
> and refinement. So, I want to use, say a given complex (having its
> coordinates + topology file, with box of waters) as a TEMPLATE and
> superimpose ONTO IT around 25 complexes of the same protein (strip off
> waters/counterions), based on C-alpha/ heavy atoms >> and get
> "modified-coordinates" of all the complexes. Does anyone have a PTRAJ
> script for this purpose.
>
> Of course, a superimposition might be done in a graphics program like
> Insight, but the hydrogen names of Insight outputs don't match with
> Amber style.....Does any one have solution to this problem, otherwise.
>
> With thanks in advance,
> Vineet
>
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