[AMBER] parmchk2 and acceptable penalty score

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in>
Date: Fri, 5 Jul 2019 22:38:49 +0530

Dear all,

I had docked mefenamic acid with a proteinand followed the sustiva tutorial
for obtaining frcmod file. which reads as follows:
---------
Remark line goes here
MASS

BOND

ANGLE

DIHE

IMPROPER
ca-ca-nh-hn 1.1 180.0 2.0 Same as X -X
-na-hn, penalty score= 41.2 (use general term))
ca-ca-ca-nh 1.1 180.0 2.0 Using the
default value
ca-ca-ca-ha 1.1 180.0 2.0 Using general
improper torsional angle X- X-ca-ha, penalty score= 6.0)
c -ca-ca-ca 1.1 180.0 2.0 Using the
default value
ca-o -c -oh 10.5 180.0 2.0 Same as X -X -c
-o , penalty score= 24.5 (use general term))

NONBON
------

Can someone please indicate if it is an acceptable penalty score..?
I am attaching the pdb file for your reference
Thank you in advance. 

-- 
Regards
 Mef_reduced.pdb
<https://drive.google.com/a/sssihl.edu.in/file/d/1csULhX8Ydntdo9xmzC3I6jMY3q7pFbdT/view?usp=drive_web>
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Received on Fri Jul 05 2019 - 10:30:02 PDT
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