From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat May 21 2011 - 09:47:49 CDT
Prathit: as the error message says, and as specified in the manual already,
you can't use ABF on orientationAngle.
Giacomo
On Sat, May 21, 2011 at 4:51 AM, Prathit Chatterjee <pc20apr_at_yahoo.co.in>wrote:
> Dear NAMD Experts,
>
> I tried to run a pmf calculation with abf as a
> function of orientation angle of the backbone of protein. I am pasting my
> input variables below -
>
> ###########################
> colvar {
> ############################################
> name tilt
> width 1.0
> lowerBoundary 0.0
> upperBoundary 180.0
> outputValue on
> outputVelocity off
> outputSystemForce off
> outputAppliedForce on
> extendedLagrangian off
>
> #############################################
>
> orientationAngle {
> atoms {
> atomNumbers 381
> atomNumbersRange 1-93953
> }
> refPositionsFile protein_nat_bb.pdb
> refPositionsCol O
> refPositionsColValue 2.0
> closestToQuaternion (1.0, 0.0, 0.0,
> 0.0) #quadruplet,the closer to (1,0,0,0) is chosen
>
> }
> }
> #########################
>
> # Bias type
> abf {
> colvars tilt
> fullSamples 100
> hideJacobian no
> outputFreq 100
> applyBias yes
> }
> ######################################
>
> I am also attaching the output file which is showing the details of
> acceptance of the variables of my colvars-input file but finally defining error
> in the colvars.
>
> Any suggestions/advice will be deeply appreciated.
>
> Thanks and regards
> Prathit Chatterjee
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:18 CST