Re: [AMBER] Penalty score

From: Henrik Hariman <>
Date: Sun, 4 Mar 2018 10:15:18 -0500

Dear David,
Thank you for your response.

On Sat, Mar 3, 2018 at 5:29 PM, David A Case <> wrote:

> On Sat, Mar 03, 2018, Henrik Hariman wrote:
> >
> > 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:
> I think your are misreading something. The existence of a penalty score
> just
> means that parmchk2 had to extrapolate to get the estimated value.
> Actually that is the point for me, then what is the difference between an
extrapolation whose penalty score is so low like 0.6 and another one whose
extrapolation is high like 70?
Do you mean that the extrapolated parameter are fine even if they have a
penalty score and even if the penalty score s high.?

> > Could not find angle parameter: n3 - cx - n3,
> This message has nothing to do with the penalty score. It looks like you
> failed to load (or load correctly) the frcmod file created by parmchk2.
> You should double-check your tleap output and leap.log file to see that the
> frcmod file is indeed being loaded into tleap.

Here is part of my tleap.bat
SUS = loadmol2 case.mol2
check SUS
loadamberparams case.frcmod

And then leap.log confirms that the files loading as they are:
> loadamberparams case.frcmod
Loading parameters: ./case.frcmod
Reading force field modification type file (frcmod)

Thank you.
Henrik Hariman

> ....dac
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Received on Sun Mar 04 2018 - 07:30:02 PST
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