ok..but what if # of atoms are different?? say i have a target RNA helix
with 841 heavy atoms, and reference helix has 844 heavy atoms (which is the
case in my structures)....how is fitting done in such cases?
Thanks
On Thu, Sep 12, 2013 at 9:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Sep 12, 2013 at 7:45 AM, Asmita Gupta <asmita4des.gmail.com>
> wrote:
> > Now, my doubt is how does ptraj go about fitting/superposing the
> structures
> > onto the reference, when the structures are not same...the chemical
> > equivalence and the no of atoms in both the structures are different..so
> > hw superposition and rms calculation is done?
>
> In ptraj, it is assumed that the mask you use selects the same atoms
> in the target as in the reference with the same ordering.
>
> In cpptraj you can specify both a target mask and a reference mask,
> which may help in your situation. As long as you ensure that the same
> # of atoms are selected with each mask the rms calculation will be
> fine.
>
> For example, say for some reason I wanted to get the RMSD between some
> atoms in a methionine (target) and a lysine (reference) residue, I
> could do something like:
>
> rms reference :MET.C,CA,N,CB,CG,SD,CE :LYS.C,CA,N,CB,CG,CD,CE
>
> The first mask is the target mask (i.e. corresponding to your input
> frames), and the second mask is for the reference.
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Thu Sep 12 2013 - 09:00:04 PDT
