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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