AMBER Archive (2008)

Subject: Re: AMBER: residual dipolar couplings - alignment tensor energy

From: Douglas Kojetin (douglas.kojetin_at_gmail.com)
Date: Tue Apr 01 2008 - 10:23:59 CDT

As a followup, I noticed the following in the output files of only the
runs with high Align (RDC) energies:

      .... RESTARTED DUE TO LINMIN FAILURE ...

      ***** REPEATED LINMIN FAILURE *****

      ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR
MORE INFO *****

I noticed that this is discussed on the AMBER FAQ page, but I'm not
sure how I should change the minimization:

"""
  Minimization

  &cntrl
     imin=1, nmropt=1,
     ntx=1, irest=0,
     ntpr=100,
     ntb=0, dielc=1, cut=10.0, scee=1.2,
     igb=1,
     ntr=0,
     maxcyc=10000, ncyc=100, ntmin=1,
     ntc=1,
     iscale=5, ipnlty=1, scalm=100, pencut=0.1,
     lastist=10000000,
  &end
  &ewald
     eedmeth=5
  &end
  &wt
     type='REST', istep1=1, istep2=2000, value1=1.0, value2=1.0,
  &end

  &wt type='END' &end

LISTOUT=POUT
DISANG=DISANG.RST
DIPOLE=RDC.RST
END
"""

Thanks in advance for any input,
Doug

On Mar 26, 2008, at 3:46 PM, Douglas Kojetin wrote:

> Hi All,
>
> I have a general question about the use of residual dipolar
> couplings during separate (1) simulated annealing and (2)
> minimization steps concerning the initial values for the Cartesian
> components (alignment tensor).
>
> I am performing a GB simulated annealing (SA) and minimization using
> 100 initial structures derived from NMR restraints, using one set of
> initial values for the alignment tensor (s11...s23) for all 100
> structures. The alignment tensor floats during the SA, and the
> coordinates are written at the end of the SA. Next for the
> minimization step, the coordinates from the SA step (where the
> alignment tensor was allowed to float) and the original dipolar
> couplings (initial alignment tensor values) are read in. Because
> the alignment tensor was allowed to float during SA, high Align
> energies (>100 kcal) are reported for some structures during and at
> the end of the last minimization step, when compared to the
> alignment tensor information (s11...s23) in the DIPOLE restraint
> file. Some structures have a more reasonable Align energy (<10
> kcal), but the energies are on average higher compared to the Align
> energies at the end of the SA step (float tensor). To resolve the
> high Align energies:
>
> (A) Should the alignment tensor information (s11...s23) in the
> DIPOLE restraint file be updated for the last minimization step to
> reflect the minimized (float) alignment tensor from the SA step?
> (B) Should I increase the number of steps of either the steepest
> descent or conjugate gradient minimization performed during the last
> minimization step to allow the tensor to float back to the original,
> initial estimate?
> (C) Should I not specify a DIPOLE restraint file in the minimization
> step?
>
> Thanks,
> Doug
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