Hi David,
Thank you so much for your instructive response!
If I’m mutating GLU to LYS, and I specify CD and beyond as the SC region, I understand that the non-SC atoms in the TI region will have a common set of coordinates. But what about the charges? TiMerge removes the “duplicates” of these atoms, so how are the two sets of charges for non-SC atoms retained? Is it?
I’d love to set up simulations where the common non-SC atoms changed charge instead of putting the entire residue into the SC region. But how can I setup the prmtop to do the former?
I’m not sure if I’m explaining this very well. Please let me know If I need to try to describe my question differently.
Thanks again for the help!
Best,
Matthew
> On Aug 29, 2022, at 4:37 PM, David A Case <david.case.rutgers.edu> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> On Mon, Aug 29, 2022, Matthew Guberman-Pfeffer via AMBER wrote:
>>
>> Is the following understanding right: the TI region is the set of all
>> transformed atoms. The SC region is the subset of TI-region atoms that
>> disappear or appear. So, in the context of an amino acid mutation, say from
>> Glu to Lys, the entire residue would be in the TI region, but only the
>> C_delta and beyond atoms of the sidechain need to be in the SC region. The
>> non-SC region TI atoms would be linearly transformed from Glu to Lys in
>> terms of their different charges, but otherwise they would remain the
>> same. Is that right?
>
> Above is correct, but may hide an additional distinction between SC atoms
> and non-SC atoms:
>
> All non-SC atoms (whether are not they are being transformed) are described
> by a single set of xyz coordinates -- the so-called "single-topology" option
> in much of the (older) literature.
>
> Atoms in the SC region use a "dual topology option".
>
> In your example, the backbone and CB/CG parts of the residue in question are
> described by a single set of coordinates, even though their charges may be
> changing as one goes from Glu to Lys.
>
> For CD and beyond, there are two sets of coordinates, one set for the Glu
> atoms, and a second set for the Lys atoms. Both sets of atoms are always
> "present", but at the end points they don't interact with the rest of the
> system, and hence are "invisible". [The Glu atoms never "see" the Lys
> atoms, but each set interacts with the rest of the system, except at the
> lambda endpoints.]
>
> There is nothing that prevents you from (say) having the entire Glu and Lys
> side chains be in the soft-core region. Decisions like this lead to
> interesting questions about convergence of the free energy calculations.
> Fortunately, there is a lot of literature to help you out.
>
> ....good luck....dac
>
>
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Received on Mon Aug 29 2022 - 14:30:02 PDT
