[AMBER] how to stop making terminal residue

From: Daniel Konstantinovsky <daniel.konstantinovsky.yale.edu>
Date: Mon, 10 Jan 2022 11:34:03 -0500

Hi Amber,

I am trying to bond a newly parameterized residue to the phosphate of a
*non-terminal* DA residue. It is non terminal in the original PDB. However,
tleap seems to make it a DA5 anyway and then it complains that the
coordination number for the resulting extra hydrogen is exceeded. How can I
force tleap *not* to treat the first DA residue in the PDB as a terminal

Thank you! I realize I have been asking a lot of questions lately. I'm
trying to parameterize a stearyl group bound to DNA and have relatively
little experience with AMBER.

- Dan
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Received on Mon Jan 10 2022 - 09:00:02 PST
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