[AMBER] Penalty score

From: Henrik Hariman <henrik.hariman.gmail.com>
Date: Sat, 3 Mar 2018 14:24:34 -0500

Dear all,

The parmchk2 gives some penalty score for some of the bonds and angles in
my case.frcmod file of the mol2 file of my system, which causes that the
tleap would not find those parameters: such as below:

~> case.frcmod
n3-cx-n3 69.346 111.230 Calculated using n3-c3-n3, penalty score=
tleap -f tleap.lt

Could not find angle parameter: n3 - cx - n3,

As I understand the lower the penalty score the better, but, I was
wondering how much should be maximally the penalty score for an entry so
that we can accept those proposed parameters for that entry and ignore the

Thank you.
Henrik Hariman
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Received on Sat Mar 03 2018 - 11:30:02 PST
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