Hi Matthew,
I'm not sure, but here's how I'd do it:
tiMerge ('mask for protein', 'mask for mutated protein', 'mask for Glu',
'mask for Lys')
The result here is that some of the atoms in Lys and Glu will have the
same coordinate (common atoms). Now in amber, you can set timask1='mask
for Glu', timask2='mask for Lys', scmask1='unique atoms in Glu',
scmask2='unique atoms in Lys'. This way, the common atoms among Glu and
Lys will be linearly transformed and the rest will be softcore. I may be
wrong, but it seems to me that "softcore" in tiMerge has the same
meaning as "timask" in amber.
Hope this helps,
Ali
On 8/30/2022 2:09 PM, David A Case via AMBER wrote:
> 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 - 15:30:03 PDT
