Dear Amber Community,
I really need help with the below and didn’t get a response several days ago when I posted, so I thought I should try posting again.
I’m trying to set up a Lys to Glu mutation where only the atoms including and beyond the delta carbon are in the softcore region. Timerge is complaining that the number of non-softcore atoms is different, but I’ve checked and that is not the case. I tried increasing the tolerance to an insane value (100.0), but that didn’t help either.
I found a post that reads almost identical to mine, but without a reply: http://archive.ambermd.org/201812/0259.html <http://archive.ambermd.org/201812/0259.html>
I’ve confirmed that (timask1)-(scmaks1) = (timask2)-(scmask2), as mentioned here: http://archive.ambermd.org/201412/0290.html <http://archive.ambermd.org/201412/0290.html>
Regarding atom ordering, I’m following “method 2” in the TI tutorial <
https://ambermd.org/tutorials/advanced/tutorial9/index.html#sidechain_mini>, where I created a lib file for the GLU (named MLU) so that the atom ordering is such that the unmatched atoms come at the end of the residue definition. I’ve attached (via a Dropbox link) the dual topology generated by TLEaP and my ParmEd input.
Can any one please help me figure out what is going wrong?
Dropbox link: https://www.dropbox.com/sh/075nvtbnmc3ar87/AACzh31u7e8xCh0k7d7EoP3Wa?dl=0 <https://www.dropbox.com/sh/075nvtbnmc3ar87/AACzh31u7e8xCh0k7d7EoP3Wa?dl=0>
Best,
Matthew
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Received on Thu Aug 04 2022 - 13:33:55 PDT
