From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Sun Jun 24 2007 - 07:30:05 CDT
Hi,
I am trying to use ABF to constrain dihedral angles. However, the script
crashes giving me an error "can't read forces(80)" etc (please see output
below). Can someone suggest something ? The ABF part of the config file and
the error output are below.
-- Maria G. Technical University of Denmark Copenhagen INPUT: ###################################### abf restraintList { d1 {dihe {PRO1 1 C} {PRO1 2 N} {PRO1 2 CA} {PRO1 2 C} 40.0 -60} d2 {dihe {PRO1 2 N} {PRO1 2 CA} {PRO1 2 C} {PRO1 3 N} 40.0 -45} } abf coordinate distance abf abf1 5 abf abf2 80 abf dxi 0.2 abf xiMin 4.0 abf xiMax 15.0 abf outFile abf_AA.pmf abf inFiles {} abf historyFile abf_AA.hist abf fullSamples 200 abf forceconst 0.0 #abf applybias no #} ###################################### OUTPUT: ###################################### CL: ABF> --------------------------------------------- TCL: ABF> Adaptive Biasing Force protocol version 1.6 TCL: ABF> --------------------------------------------- TCL: ABF> TCL: ABF> Using coordinate type : distance TCL: ABF> Distance between two atoms (beware of constraints!) TCL: ABF> dxi : 0.2 TCL: ABF> dSmooth : 0.3 [default] TCL: ABF> temp : 313 TCL: ABF> outFile : abf_AA.pmf TCL: ABF> fullSamples : 200 TCL: ABF> writeFxiFreq : 0 [default] TCL: ABF> writeXiFreq : 0 [default] TCL: ABF> abf2 : 80 TCL: ABF> fMax : 60.0 [default] TCL: ABF> outputFreq : 5000 [default] TCL: ABF> inFiles : [default] TCL: ABF> historyFile : abf_AA.hist TCL: ABF> df : 1.0 [default] TCL: ABF> moveBoundary : 0 [default] TCL: ABF> distFile : none [default] TCL: ABF> forceConst : 0.0 TCL: ABF> xiMin : 4.0 TCL: ABF> xiMax : 15.0 TCL: ABF> abf1 : 5 TCL: ABF> Accumulating force data in 55 bins TCL: ABF> Restraint d1 is a dihedral angle TCL: ABF> Atoms: (13 15 17 23) k : 40.0 kcal/mol/rad Ref: -60.0 deg TCL: ABF> Restraint d2 is a dihedral angle TCL: ABF> Atoms: (15 17 23 25) k : 40.0 kcal/mol/rad Ref: -45.0 deg Info: Entering startup phase 8 with 7244 kB of memory in use. Info: Finished startup with 7244 kB of memory in use. TCL: Minimizing for 0 steps TCL: ABF> Data written to output files at timestep 0 ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 759.2467 3014.4852 18.1991 0.0170 -4611.3194 99999999.9999 0.0000 0.0000 0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000 99999999.9999 99999999.9999 20772.8250 99999999.9999 99999999.9999 OPENING EXTENDED SYSTEM TRAJECTORY FILE TCL: Minimizing for 10000 steps TCL: can't read "forces(80)": no such variable FATAL ERROR: can't read "forces(80)": no such variable while executing "vecsub $forces($abf2) $forces($abf1)" (in namespace eval "::ABF::ABFcoord" script line 8) invoked from within "namespace eval ABFcoord { set dr [vecsub $coords($abf2) $coords($abf1)] set nv [vecnorm $dr] ;# unity vector loadtotalforces forces set df [ve..." (procedure "ABForce" line 3) invoked from within "ABForce" (in namespace eval "::ABF" script line 30) invoked from within "namespace eval ::ABF { # First timestep : we don't have forces if { $timestep == 0 } { # must not be equal to $timestep - 1 set timeStored -2 ..." (procedure "calcforces" line 2) invoked from within "calcforces" ######################################
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