Re: [AMBER] Penalty score

From: David A Case <>
Date: Sat, 3 Mar 2018 17:29:40 -0500

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.

> 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.


AMBER mailing list
Received on Sat Mar 03 2018 - 14:30:03 PST
Custom Search