AMBER Archive (2005)

Subject: Re: AMBER: bond connectivity among dummy atoms

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Mar 03 2005 - 13:57:48 CST

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       -                              -
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