On Mon, Aug 29, 2022, Matthew Guberman-Pfeffer wrote:
>
>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?
You have reached the end of my knowledge of the innards of TiMerge. I'm not
sure that the phrase "discard atoms as duplicates" is accurate, and the
end-state charges must be preserved in the prmtop file. But others on the
list will have to chime in with implementation details here.
....dac
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Received on Tue Aug 30 2022 - 14:30:04 PDT
