this is far easier in parmed, I suggest using that instead.
On Mon, Jan 22, 2024 at 1:18 PM Ge Song via AMBER <amber.ambermd.org> wrote:
> Dear Amber Community,
>
> I met a problem when modifying the topology file. I have a system
> containing a protein and a dipeptide. What I'm trying to do in the topology
> file is to set the LJ interaction between the protein and the dipeptide to
> zero.
> My strategy is: assign new indexes for the dipeptide atoms in the
> ATOM_TYPE_INDEX section, then assign new indexes for atom types pairs in
> the NONBONDED_PARM_INDEX section and then add the corresponding LJ_ACOEF
> and LJ_BCOEF. I'm very confident that my topology gives me the right LJ
> coefficients because its calculated VdW energy for the whole system equals
> to the summation of VdW energy of the protein and the dipeptide. However,
> this perfect match does not apply to the 1-4 VdWaals energy, which is
> weird. So I made some attempts, but it went more weird when I assigned the
> new indexes for dipeptide atoms in a different order, in this case, the
> calculated VdW still holds the same while the 1-4 VdWaals changes. I
> understand that for 1-4 VdWaals, Amber will use the dihedral indexes to get
> a scaling factor, but in principle this should not be related with the
> indexes in ATOM_TYPE_INDEX. Looking for some comments or suggestion.
>
> Best,
> Ge Song
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Received on Mon Jan 22 2024 - 10:30:03 PST
