Re: Free energy of conformational change

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Fri May 29 2009 - 06:44:32 CDT

Chris, Giacomo,

Likely that I can setup ABF configuration for 2.7b1. It is sufficient to
add two lines in NAMD configuration:

colvars on
colvarsConfig triiPrcol

But there is two problems minor and major:

According to namd out, next lines from colvar (and ABF) configuration
are not recognized:

fullSamples 200
hideJacobian no
outputFreq 5000
applyBias yes

But this not influence on calculation. The second fatal on calculation
is that first atom in the first group of atoms can nor be recognized, I
am trying with different definition of those atoms as 1 3 5 or 1-6
(implied centroid on the one phenyl ring) with same results. Atom
numbering are taken from input PDB file.
To be clearer, below are colvar configuartion, and below the line part
of namd out file. Please advise me to overcome the problem.
Thanks

Branko

colvar/abf configuration:

colvarsTrajFrequency 1
analysis on
fullSamples 200
hideJacobian no
outputFreq 5000
applyBias yes

colvar {

   name d

   lowerBoundary 3.88
   upperBoundary 9.60
   width 0.2

   distance {
       group1 { 1 - 6 }
       group2 { 16 17 18 }
   }
}

abf {
   colvars d
   dumpFreeEnergyFile yes
}

___________________________________-

colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 29-09-2008.
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000 [default]
colvars: # trajAppend = off [default]
colvars: The restart output state file will be
"C:\Namd\246triiPrinterASAheatdyn.restart.colvars.state".
colvars: The trajectory file will be
"C:\Namd\246triiPrinterASAheatdyn.colvars.traj".
colvars: The final output state file will be
"C:\Namd\246triiPrinterASAheatdyn.colvars.state".
colvars: # analysis = on
colvars:
----------------------------------------------------------------------
colvars: # readTrajectory = "" [default]
colvars: # readBegin = 0 [default]
colvars: # readEnd = 0 [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = d
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Error: keyword "1" is not supported, or not recognized in
this context.
colvars: If this error message is unclear, try recompile with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.

Chris Harrison wrote:
> Branko,
>
> I'm responding to your earlier email, which I marked for follow up,
> but didn't do before Giacomo replied with a very reasonable answer.
> Do you need further help with an example ABF or metadynamics input
> file or was your question resolved?
>
>
> Chris
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu <mailto:char_at_ks.uiuc.edu>
> Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
> On Wed, May 20, 2009 at 6:15 AM, Branko <bdrakuli_at_chem.bg.ac.yu
> <mailto:bdrakuli_at_chem.bg.ac.yu>> wrote:
>
> Hallo Chris,
>
> I am note the respond to Lixia, so I need something similar - to
> obtain (only) the free energy of conformational change on small
> (flexible) molecules in two explicit solvents. Using ABF on ver.
> 2.6 and defining distance between two groups of atoms in studied
> molecule works without problem, but using colvar on 2.7b1 (which
> offer plenty of possibility) looks something more complicated. So,
> please if some example of configuration file is available, let me
> know. 2.7b1 ug give more than sufficient information, but I have
> no experiences with making of input (configuration) for such
> calculations. Likely that all atoms in molecule can be used for
> free energy of conformational change evaluation.
> Thanks in advance
>
> Branko
>
>
>
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