Re: [AMBER] Superposition of 3D structures for wid type and mutants with VMD

From: Daniel Roe <>
Date: Wed, 25 Sep 2013 08:32:20 -0600


On Tue, Sep 24, 2013 at 7:46 PM, Yanyan ZHU <> wrote:
> 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?

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

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Sep 25 2013 - 08:00:03 PDT
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