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 - 10:53:55 CDT

Actually, the LINMIN FAILURE message occurs in all 100 runs, but some
runs make it further (nstep) than others and have lower Align energies
(similar energies, but higher, to that reported at the end of the
annealing run).

On Apr 1, 2008, at 11:23 AM, Douglas Kojetin wrote:

> 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
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu