Yes, I can see in my movie that all the atoms are restrained in
postions as they are connected by invisible bonds. Do you see a bond
at all between your dummy atoms and the molecule? My guess is that
this might be simply a vmd defect.
Eric
On Thu, 3 Mar 2005 14:57:48 -0500 (EST), Ilyas Yildirim
<yildirim.pas.rochester.edu> wrote:
> Hi,
>
> I have done a TI perturb from methane --> ethane. Initially I have to put
> the places of the dummy atoms. And I have to connect the dummy atoms to
> the H-atom which will transform to a C atom. Otherwise the dummy atoms
> will fly apart. When I connect them to the H-atom, they stay in the same
> place (Assuming I have created an frcmod file for the dummy atoms such
> that the force constants for the bond length, angle, dihedral angle are
> the ones used for an H-atom).
>
> Good luck.
>
> On Thu, 3 Mar 2005, Eric Hu wrote:
>
> > Hi, I had a look at the trajectory from an amber 8.0 TI perturbation
> > (molecule --> nothing) with vmd. It seems that all atoms lost
> > connectivity with each other and only spheres are shown. Is this true?
> > My question is that if I perturb part of a molecule into a new
> > functional group will this new funcional group disconnects itself from
> > the core molecule?
> >
> > It occurs to me that normally I have to manually add a bond between
> > two atoms in leap. Do I need to do so for all the dummy atoms too?
> >
> > Thanks.
> > Eric
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>
> --
> 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/ -
> ---------------------------------------------------------------
>
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Received on Thu Mar 03 2005 - 21:53:01 PST
