[gmx-users] how big the difference between two ligand can FEP handle?]

[Anton Feenstra]

QZ wrote:
> I am learning to use FEP to get the bind free energy difference between 
> two totally different ligands bound a protein. The number of atoms 
> varies between the ligands. Does gromacs require the same number of 
> atoms between sytem A and B? If not, how does the interpolation work 
> between the ligands with different atom numbers? Should I use dummy 
> atoms to match the atom numbers between the ligands? Thanks for any input.

Using this type of dummy atoms is non trivial. I am not the FEP expert,
but there may be articles on this showing how (not?) to do it.
Check especially the AE Mark or WF van Gunsteren papers (those are the
ones I know of, there may be other/better ones).


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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