[gmx-users] typeB in FEP calculations

[Rui Neves]

Hi Billy,

Thank you so much for the papers you suggested. I hadn't come across them.

However, what I would like to know is:
 At the beggining of the topology I call for all the bonded terms
('#include ffbonded.itp), and then in the [ atoms ] section, I specify the
massB, typeB and chargeB for the B-state. Do I have to explicitly write the
parameters for the B-state of the [ bonds ], [ angles ] and [ dihedrals ]
section, or are they read from the ffbonded.itp file, since I have defined
the typeB for the atoms in the B-state?

Thank you in advance for all your help.

Cheers

Rui


On 27 September 2016 at 03:18, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> 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.
>
> Cheers,
>
> Billy
>
> 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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