On Wed, Aug 24, 2011 at 2:30 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> Is there a way by which I can judiciously remove all bond-length, angle and
> dihedral angle PE terms for a chosen residue resulting in the formation of
> a
> neutral (no partial charges or unphysical) residue side-chain in Amber9.
>
In short, not fully without changing the code. You can zero out the
non-bonded interactions (charges and VDW interactions) directly in the
prmtop (I wrote a program that will do this). The problem comes when
zeroing out the bonded terms. Zeroing the force constants would eliminate
those energy terms, but then they start behaving strangely (since there are
*no* forces acting on them, you'll see inertia at play here, they'll just
fly away with their given velocity). You could modify the code to go back
after the energy/force evaluations and remove those energy terms from the
total energy, but if you have bonds stretching between the "vanished"
residue and other "non-vanished" residues, your forces won't correspond to
the hamiltonian you're using to get the energies.
If you have no such bonds, why not just create a new topology file without
that residue?
HTH,
Jason
> Any help will be highly appreciated.
>
> Thanks a lot in apprehension.
>
> Sincere regards,
> Moitrayee
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 24 2011 - 12:30:02 PDT
