[gmx-users] Edit on-the-fly topology files (stateA->stateB)

[Mark Abraham]

On 5/12/2011 12:17 AM, Vasileios Tatsis wrote:
> Greetings GrOmAcS Users,
>
> I want to calculate the free energy, for different (de)protonation 
> states, of a certain compound.
> This requires to edit by hand many topology files.
>
> Is there a code that can do it on-the-fly or any ideas(algorithm) how 
> it can be done automatically?
>

Since you'd need to add/remove the proton and perhaps change the atom 
type to which it was bound and maybe its other proton atom types, it is 
hard to come up with a general algorithm that is worth the time to 
implement.

Mark
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