In addition, if it is masses you need a way to define the position of the
particles relative to the others, and to deal with the forces. This would
not be trivial, but perhaps the needed code is available for supporting the
extra points force fields.
On Aug 9, 2011 12:25 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Aug 09 2011 - 10:00:02 PDT
