[gmx-users] typeB in FEP calculations
billy.williams-noonan at monash.edu
Tue Sep 27 04:18:58 CEST 2016
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
However, you will need to state state B terms for proper and improper
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,
> Rui Neves
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
**|* +61420 382 557
Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
More information about the gromacs.org_gmx-users