[gmx-users] Dihedral Parameters for FEP

Jose Tusell 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)?


Jose Tusell

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