[gmx-users] Dihedral Parameters for FEP
jrta1981 at gmail.com
Mon Nov 12 09:12:28 CET 2012
Dear GMX users,
I've been writing a topology for an FEP calculation on an alchemical
transformation from ASP to ASN. So far I have made a hybrid residue (D2N).
I've been modifying the topol.top file to add the parameters for the B
state. I added the atom types and charges, bonds and angles for state A
and B. When I start doing the dihedral terms I'm unsure on how to do the A
and B states since I'm using AMBER99SB.
For example: if I want to specify the following dihedral (CT CT C N) for
state A/B. When I look in the ffbonded.itp file I find two lines that
specify that dihedral:
CT CT C N 9 0.0 0.41840 4 ; phi,psi,parm94
CT CT C N 9 0.0 0.29288 2 ; phi,psi,parm94
How do I add this dihedral in the topolopy file for state A/B? Do I need
to add two lines for the same dihedral or is this done in one line?
Also I was looking at table 5.4 of the gromacs manual and I saw that only
the phi_s and k_phi can be interpolated and not the multiplicity. If the
multiplicity cannot be interpolated does this cause a problem for FEP? If
so does that mean that I would have to convert these dihedrals from type 9
(proper dihedral multiplicty) to type 3 (RB dihedral)?
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