[gmx-users] typeB in FEP calculations

Billy Williams-Noonan billy.williams-noonan at monash.edu
Tue Sep 27 04:18:58 CEST 2016

Hi there,

Because the bond and angle parameters are harmonic terms in many
forcefields, my understanding is that they should cancel out during a
closed thermodynamic cycle.  So you will not need state B parameters for
those terms.

However, you will need to state state B terms for proper and improper
dihedrals though.

Refer to the papers by Boresch, et al. from 1999.



On 27 September 2016 at 03:34, Rui Neves <rppneves at gmail.com> wrote:

> Hi Gromacs users,
> I am trying to determine a relative binding free-energy of two hypothetical
> ligands (A -> B).
> To do this, I must indicate a typeB for the atomtypes in B.
> Once this is done, do I have to explicitly include the bonded parameters
> for the B state, if I started by loading all the parameters of the force
> field that parameterizes both ligands?
> Thank you for any help,
> Regards,
> Rui Neves
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Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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