AMBER Archive (2005)

Subject: Re: AMBER: bond connectivity among dummy atoms

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Mar 03 2005 - 15:58:38 CST

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_at_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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