Hi,
I had responded to this question back on September 25, but maybe it
got lost in the shuffle. I will paste my response below.
If the two structures have the same residue numbering (e.g. both have
260 residues), you could just fit using backbone atoms. If they do not
have the same number of residues (because maybe one has a truncated
N-terminus for example) then you will need to specify a mask for both
your target and reference structures, which I'm not sure VMD can do
(the VMD mailing list may be able to help there). Howeverm the 'rms'
command in cpptraj allows you to specify both masks; as long as both
masks select the same # of atoms you can calculate an RMSD/perform RMS
best-fit etc. So, you can for example do something like:
parm wildtype.parm7 # This will correspond to parmindex 0
parm mutant.parm7 # This will correspond to parmindex 1
reference wildtype.rst7 parmindex 0
trajin mutant.rst7 parmindex 1
rms reference <mutant mask> <wildtype mask> out rmsd.mutant.to.wt.dat
Hope this helps,
-Dan
On Thu, Sep 26, 2013 at 8:16 PM, Yanyan ZHU <zhuyanzily.gmail.com> wrote:
> Dear All:
>
> I have some puzzles as following :
>
> a. VMD can not accomplish the superposition in my
> experiment, for the number of atoms in WT type and mutants are different .
>
> b. I wonder how should I do with the 3D structures of WT
> type and the corresponding mutants, to accomplish the superposition with
> VMD?
>
> Thank you very much for your kindhearted and give my best wishes to you.
>
>
>
>
> Yanyan Zhu
> Sichuan university, China
>
>
> September 27.2013
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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) 585-6208 (Fax)
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Received on Fri Sep 27 2013 - 08:00:02 PDT
