Hi David,
I think I can re-phrase my question in a better way.
Let’s say I’m mutating Glu to Lys and I only want the CD and beyond atoms in the SC region. So, my timask and scmasks would look like the below
timask1=‘.3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,3645,3646’
scmask1=‘.3644,3645,3646’
timask2='.8795,8796,8797,8798,8799,8800,8801,8802,8803,8804,8805,8806,8807,8808,8809,8810,8811,8812,8813,8814,8815,8816'
scmask2='.807,8808,8809,8810,8811,8812,8813,8814,8815,8816'
The common non-softcore atoms that need their charges transformed are
.3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643
.8795,8796,8797,8798,8799,8800,8801,8802,8803,8804,8805,8806
My question is: If you use TiMerge, it will discard the @8795-8806 set of atoms as duplicates. Does that also throw away the final-state charges?
If I don’t use TiMerge, then the .3632-3643 and .8795-8806 sets of atoms will interfere with one another, right?
Unless I just put everything in the softcore region, I don’t know how to set up the prmtop for these non-softcore TI atoms. Any suggestions? How can I transform the charges of these otherwise common atoms to the Glu (before state) and Lys (after state) for the mutation?
Best,
Matthew
> On Aug 29, 2022, at 5:25 PM, Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> 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 - 19:00:02 PDT
