[AMBER] ParmEd, Trouble with timerge

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Thu, 30 Jun 2022 10:05:12 -0400

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>


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Received on Thu Aug 04 2022 - 13:33:55 PDT
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