There is no way of doing this currently in Amber. I've written a prmtop
editor program that will make this possible, which I think may be included
in the next AmberTools release (if it makes the cut).
What you would have to do is to create your library file from a template
(mol2 file, or use saveoff in tleap after constructing your benzene residue
the way you want it). Then you have to make an frcmod file that includes
the bonded parameters to your new atom type (to which you assign 0 mass,
though you may have to make it 0.000001 since i think the inverse of the
mass is used in some places), and a VDW radius/depth of 0 and a charge of 0.
What my program will enable is for you to specifically define your new atom
type's VDW interactions with itself to have its own combined depth and
radius value that will give it a non-zero VDW interaction, but all other
interactions between that atom type and other atom types will remain
unchanged (that is, they'll be 0).
Note that there's no way of doing the same thing for electrostatic
interactions with modifying the code yourself, so keep this in mind if you
wanted these fictitious particles to have EEL interactions with each other
but not with anybody else.
If you're interested in the program, contact me off-list.
HTH,
Jason
On Tue, Aug 9, 2011 at 11:20 AM, Tan Yaw Sing <tanys.bii.a-star.edu.sg>wrote:
> Hi Amber users,
>
> I would like to add a massless particle to benzene. This particle should
> not
> interact with any other atoms in the system except for similar massless
> particles on other benzene molecules. How should I do it? I am
> considering
> creating a frcmod file but there seems to be no provision for restricting
> the vdw interactions of an atom under the "nonbonded" section.
>
> Thanks,
> Yaw Sing
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 09 2011 - 09:30:04 PDT
