[AMBER] paramfit - negative energy for 1 of the 2 term

From: Erdem Yeler <erdemyeler.gmail.com>
Date: Thu, 21 May 2020 15:26:07 +0300

I parameterized some dihedrals with paramfit here is the result:

oz-Z3-ob-ca 1 -1.2200 180.000 -1.000
oz-Z3-ob-ca 1 4.2000 180.000 2.000

AS you can see for the same dihedral one term has a negative Kn value
(-1.2200) . Here, http://archive.ambermd.org/201602/0206.html Robin said
"negative bond energy is a problem..." Actually in my case, there are 2
terms for the same parameter but I hesitated about my parameters. is it a
problem if one of the two terms for the same dihedral has negative energy?
Can I use them? (By the way, minimized structure with this parameter was
perfect: RMSD between minimized structure and X-ray experimental structure
was 0.0003)
Best regards,
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Received on Thu May 21 2020 - 05:30:02 PDT
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