Re: [gmx-users] typeB in FEP calculations

[Rui Neves]

Thank you very much for your help.
I think that I finally got this straight.

Cheers,

Rui

On 27 September 2016 at 11:26, Hannes Loeffler 
wrote:

> On Tue, 27 Sep 2016 11:08:45 +0100
> Rui Neves  wrote:
>
> > 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?
>
> If you wish to have the same parameters (for non-changing bonded terms)
> there is not need to fill in the B state. However, if the bonded
> parameters change, your topology file will necessarily have to reflect
> this and you need to change the B state accordingly.  Grompp doesn't
> make any assumption as to what you want esp. in the case of
> disappearing/appearing atoms (where the typically approach is to take
> the parameters from the other state i.e. the one where the bonded term
> exists).  For torsions Gromacs would require a term-by-term matching
> (same periodicities).
>
> Cheers,
> Hannes.
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Re: [gmx-users] typeB in FEP calculations

[Hannes Loeffler]

On Tue, 27 Sep 2016 11:08:45 +0100
Rui Neves  wrote:

> 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?

If you wish to have the same parameters (for non-changing bonded terms)
there is not need to fill in the B state. However, if the bonded
parameters change, your topology file will necessarily have to reflect
this and you need to change the B state accordingly.  Grompp doesn't
make any assumption as to what you want esp. in the case of
disappearing/appearing atoms (where the typically approach is to take
the parameters from the other state i.e. the one where the bonded term
exists).  For torsions Gromacs would require a term-by-term matching
(same periodicities).

Cheers,
Hannes.
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Re: [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-noo...@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  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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
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>
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>
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Re: [gmx-users] typeB in FEP calculations

[Billy Williams-Noonan]

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  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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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