[AMBER] timask vs. scmask question

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Mon, 29 Aug 2022 09:58:52 -0400

Dear Amber Community,

I’m a bit confused by the timask vs. scmask distinction. I’ve discussed this already with one of you (Saikat Pal), but wanted to ask more generally.

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?

If so, when I use timerge in ParmEd, why does it print out the same mask for timask and scmask?

Best,
Matthew






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Received on Mon Aug 29 2022 - 07:00:06 PDT
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