On Fri, Nov 07, 2025, Surabhi Singh 24933024 wrote:
>Got the exact issue, it's the Phosphate group at 5'ends of the DNA that was
>giving bad contact.
>
Is the bad contact between the H atom on the phosphate group and a
neighboring oxygen atom on the same phosphate?
If so, that is a problem that we have seen before, and the "fix" involves
increasing the force constant on the P-O-H angle. I don't remember the
details right now, but let us know if this is the bad contact -- we can
track things down, and others on the list probably have better grey cells
than I have.
If it's not this, knowing which atoms are involved in the bad contact might
trigger some thoughts. That's assuming that you have not already made
progress on your own.
...good luck...dac
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Received on Fri Nov 07 2025 - 08:30:03 PST
