alpha pmf

From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Wed May 04 2011 - 00:55:40 CDT

Dear NAMD Experts,                        I am trying to find out the potentials of mean force with respect to the helicity fraction of a portion of the protein through ABF. The colvar config file is listed below - #Global options: colvarsTrajFrequency    100 colvarsRestartFrequency 2 analysis                off ########################### colvar {         ############################################         name                    hlx_frac         width                   1.0         lower boundary          0.0         upper boundary          1.0         outputValue             on         outputVelocity          off         outputSystemForce       off         outputAppliedForce      off         extendedLagrangian      off         alpha {                 residueRange    71-82                 psfSegID        ASYN                 hBondCoeff      0.5                 angleRef        88                 angleTol        15                 hBondCutoff     3.3                 hBondExpNumer   6                    hBondExpDenom   8                 atomsFile       hlx_frac.pdb                 atomsCol        O                 atomsColValue   2.0         } } ############################################# # Bias type abf {         colvars         hlx_frac         fullSamples     100         hideJacobian    no         outputFreq      100         applyBias       yes } ###################################### The error message which is coming in the output file is - colvars:     Error: cannot add atoms to a dummy group. colvars:     If this error message is unclear, try recompiling with -DCOLVARS_DEBUG. FATAL ERROR: Error in the collective variables module: exiting. Any kind of suggestion or correction will be highly appreciated. Thanks and regards Prathit Chatterjee

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