[AMBER] sviol script error ?

From: Benjamin Chagot <Benjamin.Chagot.univ-lorraine.fr>
Date: Wed, 14 Dec 2016 17:08:52 +0100

Dear Amber Users,

I tried to analyse protein's restrained molecular dynamic and while
parsing sander output I got issues.

Amber14 (and 16) version of the sviol script seems to forget to report
violations compared to an "older" sviol version (amber11) : negative
angle restraints are not reported.

To make it works I had to modify line 179 i.e. :

                #if ($_ =~
/(.{34})\s+[\d\.]+\s+([\d\.]+)\s+([\d\.]+)\s+[\d\.]+ (\w)\s+/) {
                 if ($_ =~
/(.{34})\s+[\-?\d+.\d+]+\s+(\-?\d+.\d+)\s+(\-?\d+.\d+)\s+[\d\.]+ (\w)\s+/) {

The perl code is maybe not perfect but it is working on my outputs.



Benjamin Chagot

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Received on Wed Dec 14 2016 - 08:30:02 PST
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