[AMBER] About statistical report of 'RMS deviation from ideal bonds/angles'

From: Yi Zhang <zhang_yi.pku.edu.cn>
Date: Wed, 21 Jan 2015 16:13:09 +0800

Dear All,

I was trying to evaluate the NMR structure ensemble refined using AMBER9
based on NOE distance and angle restraints. However, I could not find the
statistical report of 'RMS deviation from ideal bonds/angles'. On the web
page (http://ambermd.org/Questions/nmr.html), it was suggested that we could
directly read the statistics at the end of the violation list. However, I
can't find these reports in the output files. Does anyone know how to fix

Thank you very much for your help.

Best regards,



The input annealing protocol:


    nstlim=30000, pencut=-0.001, nmropt=1,

    ntpr=100, ntwx=100,ntt=1, cut=12.0,

    ntc=1, vlimit=20., scee=1.2, igb=5, ntb=0,



&wt type='TEMP0', istep1=0, istep2=8000, value1=1000.0, value2=1000.0, &end


&wt type='REST', istep1=16001, istep2=30000, value1=1.0, value2=1.0, &end

&wt type='END' &end




And the output (for a single structure, in the overview/.o file):

  H VAL 271 -- H CYS 250: 6.597 6.500 0.097 0.186 d

                                       Total distance penalty: 69.715

                                       Total torsion penalty: 7.300

AMBER mailing list
Received on Wed Jan 21 2015 - 00:30:02 PST
Custom Search