[gmx-users] Relative FEP topology question - What to do with state B dummy atoms in the .itp file under [ bonds ], [ angles ] and [ dihedrals ]
letmeposttoyourmailinglist at gmail.com
Wed May 4 04:00:32 CEST 2016
Hi Gromacs Users,
Just some background - I am doing FEP to determine the difference in
binding free energy between two ligands (state A and state B) wherein state
A has an isopropyl ether group and state B has a methyl ether group in its
place. In other words I am transmuting the isopropyl group into a methyl
I am using a united atom topology file for my ligands and the GROMOS 96
forcefield. Ligand topologies come from the ATB.
The difference in dG between these two states should be +7.04, from
literature. I am not currently getting this value, not even within an RMSD
of 10 kJ/mol.
In transfiguring the isopropyl (state A) into the methyl moiety (state B),
I have set the two CH3 and one H groups from state A into DUM atom types in
state B, and likewise transfigured the central carbon of the isopropyl
group, a C atom type, into a CH3 atom type. I have re-adjusted the charges
on every state B atom for the state B ligand where necessary.
My question is this - how do I state that the [ dihedral ] angles, [ angle
] and [ bonds ] from the CH3, CH3 and H atom types annihilated, no longer
exist in State B, under the [ dihedral ], [ angle ] and [ bonds ]
I have consulted the gromacs manual (section 5.7.4), but the table (table
5.6) and information included do not answer my question. Or the table
(table 5.6) might have the information I need, but it is unclear what the
table is saying. The example provided is also too simplistic (propanol to
pentane) and I need to know what to do in my case.
I've been told that even non-interacting atoms can contribute energy by
virtue of their rotation so any advice on what to do would be greatly
Please let me know if you need more information.
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