extensions/analysis/RMSDcalculator
for more details check the vmd manual or web pages.
I also recommend installing the RMSDTT (do
a web search for vmd and rmsdtt)
S.Sundar Raman wrote:
> thanks for your comments, i checked in VMD, it displays correctly, but
> i don't know how to superimpose structures in VMD. pls help me in this
> regard
>
> On 12/1/05, *Ilyas Yildirim* <yildirim.pas.rochester.edu
> <mailto:yildirim.pas.rochester.edu>> wrote:
>
> Dear Raman,
>
> Do u use the trajectory file (.mdcrd) or the restart file (.rst)
> to create
> the .pdb files? For the second case, using ambpdb will create the
> correct
> .pdb file. Do u use the following command to create it?
>
> ambdpdb -p molecule.prmtop <molecule_min.crd> molecule_min.pdb
>
> where molecule.prmtop is the topology file, molecule_min.crd is the
> minimized restart file and molecule_min.pdb is the .pdb file of the
> minimized structure.
>
> Did u try to check these structures in VMD? In InsightII, it is
> normal if
> it will show u a different structure, as it uses its library to
> define the
> residues. Check out molecule_min.pdb. The atom names, the residue
> names
> might look different than the residue library of InsightII. But I
> never
> had any trouble in VMD. Try to check those minimized structures in
> VMD.
>
> Good luck,
>
> On Thu, 1 Dec 2005, S.Sundar Raman wrote:
>
> > dear amber friends,
> > i like to get structures from MD file at several snapshots, i
> used ptraj
> > command to get that and then i used sander to remove the kinetic
> energy by
> > minimize those structures. in order to align these structures i
> need the
> > minimized coordinates in pdb format. hence i used ambpdb command
> to convert
> > crd files which was minimized, to pdb file.( i used the topology
> file!).
> > when i viewed the generated pdb file in pymol, insightII, and
> moil-view it
> > showed the atoms connected very wrongly. but when i use ptraj
> to generate
> > pdb file form the same topology and crd file, it produces correctly
> > connected pdb file. why this kind of problem appears? pls help
> me in this
> > regard. thank you
> >
> > --
> > S.Sundar Raman
> > Chemical Lab,
> > CLRI
> > Chennai-20
> > ph: 044-24411830
> >
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/
> <http://www.pas.rochester.edu/%7Eyildirim/> -
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
>
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>
>
>
>
> --
> S.Sundar Raman
> Chemical Lab,
> CLRI
> Chennai-20
> ph: 044-24411830
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Received on Thu Dec 01 2005 - 14:53:01 PST
