Message: 6
Date: Mon, 30 May 2016 16:38:10 +0200
From: Vasantha Kumar <vin.vasanth.gmail.com>
Subject: [AMBER] NMR restraints violation limit
To: Amebr Mailing List <amber.ambermd.org>
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<CAKY45+sehn912XyAUZZ=P0o99Bi08B--Prj2LbSsfUaBU19MOw.mail.gmail.com>
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Dear Amber user
I have a question on the violation of limit of NMR restraints in amber
structure calculation. Below is a out put file that I have got sviol2
command. If I understood correctly mean is my deviation from the target
value (bin). In my case I have 0.2+/-0.05 A? violation my questions is
are these in the allowed limit. My system is chimeric in addition to NOEs
there is also contribution from the quality of the force field. Could any
one suggest me whats is the allowed violation limit (mean) for a routine
NMR calculated stuctures.
thanks
Vince
PS: vilations
---------------------------------------------------------------
#viols mean bin first atom second atom xpkno
---------------------------------------------------------------
1 0.211 3.500 H ALA 12 -- H ARG 13 0:
1 0.198 3.000 N OUH 22 -- O OUH 19 0:
1 0.197 2.200 HN2 OUK 20 -- O OUR 18 0:
1 0.197 2.200 H OUH 22 -- O OUH 19 0:
1 0.190 3.500 HA OUR 18 -- HN2 OUR 18 0:
1 0.187 2.500 H OUK 17 -- HN2 OUE 16 0:
1 0.182 2.200 HN2 OUH 22 -- O OUK 20 0:
?
------------------------------
Hi Vince
You are correct, sviol2 reports the mean deviation from the target value. This may be the upper or lower limit of the restraint, depending which side was violated.
Deciding what is an acceptable violation is totally up to you. I would suggest looking at several recent NMR structure papers to see what they report. If, as you say, you have an additional contribution to the violations from the force field, you can argue that a larger mean violation is acceptable.
Brendan
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Received on Tue May 31 2016 - 12:30:03 PDT
