Re: [AMBER] NMR refinment issues

From: <>
Date: Thu, 15 Apr 2010 15:54:32 -0400

I think that CALIBA uses "center" average for conversion to its upper distance constraints so i changed ir6=1 to 0 in my RST file since the manual says that 0 is for center averaging (pg 176). When i do this using the script in my previous post, my temperature kept going up past 1000K all the way up to around 1900K. Is there another flag that should be set so that them follows the script? Thanks



-----Original Message-----
Sent: Wed, Apr 14, 2010 11:17 am
Subject: [AMBER] NMR refinment issues

First time AMBER user here and am using it for NMR refinement presently.

I followed the DNA protocol in the tutorial section and have everything working
just fine however im having some issues with the end results. Im using the
CALIBA macro from CYANA to cailbrate my peaklists to upper distance limits and
when i run refinement using this anneal script

simulated annealing protocol, 30 ps
    nstlim=15000, pencut=-0.02, nmropt=1,
    ntpr=200, ntt=1, ntwx=200,
    cut=12.0, ntb=0, vlimit=12, rgbmax=12.0,
    igb=1, saltcon=0.2,
#Simple simulated annealing algorithm:
#from steps 0 to 5000: heat the system to 600K
#from steps 5001-18000: re-cool to low temperatures with long tautp
#from steps 18001-20000: final cooling with short tautp
 &wt type='TEMP0', istep1=0,istep2=1000,value1=10.,
            value2=1000., /
 &wt type='TEMP0', istep1=1001, istep2=3000, value1=1000.0,
            value2=1000.0, /
 &wt type='TEMP0', istep1=3001, istep2=15000, value1=0.0,
            value2=0.0, /
 &wt type='TAUTP', istep1=0,istep2=3000,value1=0.2,
            value2=0.2, /
 &wt type='TAUTP', istep1=3001,istep2=11000,value1=4.0,
            value2=2.0, /
 &wt type='TAUTP', istep1=11001,istep2=13000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=13001,istep2=14000,value1=0.5,
            value2=0.5, /
 &wt type='TAUTP', istep1=14001,istep2=15000,value1=0.05,
            value2=0.05, /
 &wt type='REST', istep1=0,istep2=3000,value1=0.1,
            value2=1.00, /
 &wt type='REST', istep1=3001,istep2=15000,value1=1.00,
            value2=1.00, /
 &wt type='END' /
i get small penalty values overall (~20) which from the litierature ive read is
normal. However my the issue with my RMSD of the final structure, it ends up
being around 1.2 which is pretty high since it comes out from CYANA being around
.6 or so. Im not sure if my constraint upper limits are a little loose or not.
Ive tried other methods of calibration using the "peaks calibrate" macro in
CYANA which leaves my RMSD low (~0.6) but my penalties are huge (~200) or so.
I know this is more of an NMR question so maybe some users of CYANA and AMBER
can help me out and maybe some explanation. Thanks for your help and let me
know if you need some more information.


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Received on Thu Apr 15 2010 - 13:00:04 PDT
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