All right. Thank you, Ilyas.
Regards,
-Eric
On Thu, 3 Mar 2005 16:58:38 -0500 (EST), Ilyas Yildirim
<yildirim.pas.rochester.edu> wrote:
> No, I dont see the bonds in vmd. But they are restrained in those
> positions I want. I think the reason is because of the dummy atoms. VMD (I
> guess) does not know anything about dummy atoms. In my case, I labeled
> them as DH, and VMD would not understand what that means. Also, when I do
> the perturbation at lambda=0 (which is the methane case), I should not
> expect to have bonds between the dummy atoms and the H (which will
> transform to C at the end).
>
> Another thing, when I load the info.s in vmd, I use the initial .parmtop
> file which has the dummy atoms info in it. So, even when I do the
> perturbation at lambda=1 (which is ethane), I dont see the bonds. And I
> think the reason is because of the .parmtop file. It has the initial
> structure information (which is methane and dummy atoms) and the
> perturbation informations. But I think vmd cannot understand (or combine
> the perturbation info with the structure) the perturbation infos.
>
> Best,
>
> On Thu, 3 Mar 2005, Eric Hu wrote:
>
> > 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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>
> --
> 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 - 22:53:01 PST
