Hi Mariano,
Can you specify more details about "treating the two ligands as different” and what is its difference from the previous settings you chose?
Pengfei
> On Sep 18, 2020, at 10:41 AM, Mariano Curti <mcurti.iciq.es> wrote:
>
> Dear all,
>
> I've found unexpected behavior from LEaP (Amber 18), thus would be
> grateful if you help me determine whether this is a mistake from my
> part, or a bug in the program.
>
> I'm using MCPB.py to build parameters for a metal-containing ligand that
> is covalently attached to a protein. When using only one of these
> ligands, everything works well. However, when I include two ligands,
> while LEaP builds the dihedral parameters list correctly for the first
> ligand, it (wrongly) includes additional dihedrals for the second ligand.
>
> A reduced tLEaP input that reproduces this behavior is as follows. Note:
> I have derived the metal-related parameters using MCPB.py for one
> ligand, but the second is identical, so I use the same set. In this
> example the two first residues are the first ligand, while residues 3
> and 4 are the second ligand. I omitted the protein since it does not
> affect this problem.
>
>
> source leaprc.gaff
> addAtomTypes {
> { "M1" "Zn" "sp3" }
> { "Y2" "N" "sp3" }
> { "Y3" "N" "sp3" }
> { "Y4" "N" "sp3" }
> { "Y5" "N" "sp3" }
> }
> ZN1 = loadmol2 ZN1.mol2
> PZ1 = loadmol2 PZ1.mol2
> loadamberparams PPZ.frcmod
> loadamberparams complex_mcpbpy.frcmod
> mol = loadpdb complex.pdb
> bond mol.1.ZN mol.2.N
> bond mol.1.ZN mol.2.N1
> bond mol.1.ZN mol.2.N2
> bond mol.1.ZN mol.2.N3
> bond mol.3.ZN mol.4.N
> bond mol.3.ZN mol.4.N1
> bond mol.3.ZN mol.4.N2
> bond mol.3.ZN mol.4.N3
> saveamberparm mol complex.prmtop complex.inpcrd
>
>
> When looking at the resulting prmtop, I notice that there are extra
> dihedral parameters (with non-zero force constants) involving the metal
> of the second ligand. At the end of the day, this seems to result in
> weird MMGBSA results.
>
> Now, if I follow the same steps, but this time treating the two ligands
> as different (i.e. renaming the residues so LEaP thinks they are
> different), I get the expected prmtop, with matching dihedral parameters
> for both ligands.
>
> My question is, then: am I doing something wrong, or this is a bug in
> LEaP? I would be happy to provide any necessary additional information
> or files.
>
> Many thanks in advance!
>
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Received on Thu Oct 22 2020 - 14:30:03 PDT
