[AMBER] NMR refinment issues

From: <rolandmarques.aol.com>
Date: Wed, 14 Apr 2010 12:17:44 -0400

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.


AMBER mailing list
Received on Wed Apr 14 2010 - 09:30:04 PDT
Custom Search