From: Paulo Cesar Telles de Souza (paulocts_at_gmail.com)
Date: Wed Sep 02 2009 - 10:55:19 CDT
Dear Jerome
Thanks a lot for your help! I didn't know that the NAMD 2.7b1 altered ABF
method (and others) in such a way. I have decided to use this new version of
NAMD with colvars module. I don't think that it is necessary employing
multidimensional ABF for my problem. I have obtained PMF using a SMDs and
Jarzynski equality and now I would like to compare the result with one
obtained using another free energy calculation method. To specify the same
reaction coordinate that I have used in SMD, I have tried to use the
distance component, that is, I chose ligand atoms for group 1 and dummyAtom
option for group 2 (setting the appropriate coordinate to reproduce the same
reaction coordinate), but, still, it didn't work. I pasted the error message
below. Is it necessary to use another option together with dummyAtom?
Bests,Paulo
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 29-09-2008.
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 500
colvars: # trajAppend = off [default]
colvars: The restart output state file will be "protabf-a.colvars.state".
colvars: The trajectory file will be "protabf-a.colvars.traj".
colvars: The final output state file will be "protabf-a.colvars.state".
colvars: # analysis = off [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = Distance
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 35 atoms, total mass = 650.977.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 0 atoms, total mass = 1.
colvars: All components initialized.
colvars: # width = 0.1
colvars: # lowerBoundary = 16
colvars: Lower boundary defined.
colvars: # upperBoundary = 31
colvars: Upper boundary defined.
colvars: # lowerWallConstant = 10
colvars: Applying a harmonic lower wall at 16, with coefficient 10.
colvars: # upperWallConstant = 10
colvars: Applying a harmonic upper wall at 31, with coefficient 10.
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ------------------------------
----------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { Distance }
colvars: # applybias = on [default]
colvars: # hidejacobian = off [default]
colvars: Jacobian (geometric) forces will be included in reported free
energy gradients.
colvars: # fullsamples = 500
colvars: # inputprefix = [default]
colvars: # outputfreq = 500 [default]
colvars: Finished ABF setup.
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
Info: Startup phase 7 took 0.012846 s, 7.72452 MB of memory in use
Info: Startup phase 8 took 0.000380039 s, 12.3929 MB of memory in use
Info: Finished startup at 0.541487 s, 12.3929 MB of memory in use
TCL: Running for 4000000 steps
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 849.8375 2408.4881 1348.5871
135.3159 -5237.1600 -1091.2560 0.0000
0.0000 3104.3467 1518.1595 292.6250 -1586.1873
1557.9272 292.6250 112.1152 111.0410
590148.0000 112.1152 111.0410
colvars: Error: system forces are not available from a dummy atom group.
colvars: If this error message is unclear, try recompile with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
[0] Stack Traceback:
[0] CmiAbort+0x7f [0xa4526d]
[1] _Z8NAMD_diePKc+0x62 [0x500082]
[2] _ZN16colvarproxy_namd11fatal_errorERKSs+0x64 [0x844b68]
[3] _ZN12colvarmodule11fatal_errorERKSs+0x18 [0x79ae22]
[4] _ZNK12colvarmodule10atom_group12system_forceEv+0x53 [0x816f75]
[5] _ZN6colvar8distance19calc_force_invgradsEv+0xd7 [0x829145]
[6] _ZN6colvar4calcEv+0xc03 [0x7cca1f]
[7] _ZN12colvarmodule4calcEv+0x6c [0x7969bc]
[8] _ZN16colvarproxy_namd9calculateEv+0x497 [0x8415a1]
[9] _ZThn16_N16colvarproxy_namd9calculateEv+0xa [0x841108]
[10]
_ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x71
[0x77b165]
[11] _ZN18GlobalMasterServer11callClientsEv+0x469 [0x77f191]
[12] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x6f7
[0x77e7d7]
[13] _ZN10ComputeMgr21recvComputeGlobalDataEP20ComputeGlobalDataMsg+0x12
[0x569388]
[14]
_ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0xf
[0x569373]
[15] CkDeliverMessageFree+0x21 [0x9c2d71]
[16] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c2365]
[17] CsdScheduleForever+0xa5 [0xa4bcf5]
[18] CsdScheduler+0x1c [0xa4b8f6]
[19] _ZN7BackEnd7suspendEv+0xb [0x508add]
[20] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x140 [0x8fcde4]
[21] TclInvokeStringCommand+0x91 [0xa6e208]
[22] namd2 [0xaa4058]
[23] Tcl_EvalEx+0x176 [0xaa469b]
[24] Tcl_EvalFile+0x134 [0xa9c0a4]
[25] _ZN9ScriptTcl3runEPc+0x14 [0x8fc4e2]
[26] _Z18after_backend_initiPPc+0x22b [0x50481b]
[27] main+0x3a [0x5045ba]
[28] __libc_start_main+0xe6 [0x7ff4b89e8466]
[29] _ZNSt8ios_base4InitD1Ev+0x52 [0x4ff9ea]
Charm++ fatal error:
FATAL ERROR: Error in the collective variables module: exiting.
Aborted
2009/8/31 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> Dear Paulo,
>
> About your doubt: it is not easy to describe ligand-receptor binding
> with a single parameter. Sop far, I am not aware of anyone
> successfully applying ABF to a protein-ligand binding problem. You may
> have better luck with a multidimensional calculation, using either ABF
> or metadynamics.
>
> About your problem: indeed, there seems to be an error in the
> documentation for the abscissa parameter. As mentioned prominently on
> the webpage you link to, the NAMD 2.6 ABF code is deprecated, and only
> the colvars module of NAMD 2.7b1 is actively maintained. If you cannot
> use NAMD 2.7b1, one option is to modify the abscissa.tcl script to
> accept an atom group for abf3 rather than a single atom. This should
> be relatively straightforward. However, it will not solve the problem
> of choosing the right coordinate(s) for the job.
>
> Best,
> Jerome
>
>
> On Mon, Aug 31, 2009 at 12:00 PM, Paulo Cesar Telles de
> Souza<paulocts_at_gmail.com> wrote:
> > Dear all,
> >
> > I have some doubts and one problem on running ABF simulations in NAMD.
> >
> > Doubts: I'm not sure what order parameter is better for my system, mainly
> > because I have tested to use the z-coord order parameter and it didn't
> work.
> > I selected some atoms in the binding site (abf1) and the ligant atoms
> > (abf2). The z axis of the box is parallel to the direction from the
> ligand
> > in the receptor to the solvent bulk and the distance vector between abf1
> and
> > abf2 is almost parallel to the z-direction. For my suprise, when I
> performed
> > the ABF simulation, the ligant "walk'' in the protein surface. Did I
> choose
> > the wrong order parameter or the problem is due to my vector abf1-abf2 ?
> > Does the vector abf1-abf2 change during ABF simulations ?
> >
> > Problem: I have tried to use the abscissa order parameter to obtain a PMF
> > along a dissociation pathway through which a ligand unbinds from its
> > receptor (the reaction coordinate is ligant-protein to ligant-solvent). I
> > used a group of atoms in abf3 but received the following message error.
> This
> > is strange because the manual and this repository
> > (http://www.edam.uhp-nancy.fr/ABF/repository.html) specify that I can
> choose
> > a list of atoms. If I try only with one atom, it works. How can I use a
> list
> > in abf3 ( I want that a entire system to move along the vector defined by
> > abf1 and abf2) ?
> >
> > Thanks on advance
> >
> > Paulo
> >
> > TCL: ABF> ---------------------------------------------
> > TCL: ABF> Adaptive Biasing Force protocol version 1.7
> > TCL: ABF> ---------------------------------------------
> > TCL: ABF>
> > TCL: ABF> Using coordinate type : abscissa
> > TCL: ABF> Position of an atom along the axis joining two groups
> > TCL: ABF> dxi : 0.1
> > TCL: ABF> outFile : abf.dat [default]
> > TCL: ABF> fullSamples : 500
> > TCL: ABF> writeFxiFreq : 0 [default]
> > TCL: ABF> writeXiFreq : 100
> > TCL: ABF> abf2 : 4240 4241 4242 4243 4244 4245
> > TCL: ABF> fMax : 60.0 [default]
> > TCL: ABF> outputFreq : 5000 [default]
> > TCL: ABF> inFiles : [default]
> > TCL: ABF> historyFile : none [default]
> > TCL: ABF> df : 1.0 [default]
> > TCL: ABF> moveBoundary : 0 [default]
> > TCL: ABF> distFile : none [default]
> > TCL: ABF> temp : 300.0 [default]
> > TCL: ABF> forceConst : 10.0
> > TCL: ABF> dSmooth : 0.1
> > TCL: ABF> xiMin : -1.0
> > TCL: ABF> xiMax : 15.0
> > TCL: ABF> abf1 : 2724 2725 2726 2727 2728 2729 2730 2731 2732
> > 2733 2734 2735 2736 2737 2738 2739 2806 2807 2808 2809 2810 2811 2812
> 2813
> > 2814 2815 2816 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827
> 2828
> > 2829 2830 2831 3040 3041 3042 3043 3044 3045 3046 3047 3048 3049 3050
> 3051
> > 3052 3053 3054 3055 3056 3103 3104 3105 3106 3107 3108 3109 3110 3111
> 3112
> > 3113 3114 3115 3116 3117 3118 3119 3120 3121 3418 3419 3420 3421 3422
> 3423
> > 3424 3425 3426 3427 3428 3429 3430 3431 3432 3433 3434 3435 3436 3437
> 3438
> > 3439 3440 3441 3497 3498 3499 3500 3501 3502 3503 3504 3505 3506 3507
> 3508
> > 3509 3510 3511 3512 3513 3514 3515
> > TCL: ABF> Accumulating force data in 160 bins
> > TCL: ABF> Moving abf.dat to abf.dat.BAK
> > TCL: ABF> Using the abscissa of atom 4240 4243
> > TCL: expected integer but got "4240 4243"
> > FATAL ERROR: expected integer but got "4240 4243"
> > while executing
> > "addatom $abf3"
> > (in namespace eval "::ABF::ABFcoord" script line 9)
> > invoked from within
> > "namespace eval ABFcoord {
> >
> > set abf1 $::ABF::abf1
> > set abf2 $::ABF::abf2
> > set abf3 $::ABF::abf3
> >
> > print "ABF> Using the abscissa of atom $abf3"
> >
> > adda..."
> > (procedure "ABFstartup" line 2)
> > invoked from within
> > "ABFstartup"
> > (in namespace eval "::ABF" script line 4)
> > invoked from within
> > "namespace eval ::ABF {
> >
> > # coordinate-specific startup procedure
> > ABFstartup
> >
> > if { [info exists restraintList] } {
> >
> > array set rArray $restraintList
> > ..."
> > (file "/home/paulo/Desktop/Tutorial-ABF/abf-1.8/abf_script.tcl" line
> > 766)
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: expected integer but got "4240 4243"
> > while executing
> > "addatom $abf3"
> > (in namespace eval "::ABF::ABFcoord" script line 9)
> > invoked from within
> > "namespace eval ABFcoord {
> >
> > set abf1 $::ABF::abf1
> > set abf2 $::ABF::abf2
> > set abf3 $::ABF::abf3
> >
> > print "ABF> Using the abscissa of atom $abf3"
> >
> > adda..."
> > (procedure "ABFstartup" line 2)
> > invoked from within
> > "ABFstartup"
> > (in namespace eval "::ABF" script line 4)
> > invoked from within
> > "namespace eval ::ABF {
> >
> > # coordinate-specific startup procedure
> > ABFstartup
> >
> > if { [info exists restraintList] } {
> >
> > array set rArray $restraintList
> > ..."
> > (file "/home/paulo/Desktop/Tutorial-ABF/abf-1.8/abf_script.tcl" line
> > 766)
> >
> > [0] Stack Traceback:
> > [0] CmiAbort+0x7f [0xa4526d]
> > [1] _Z8NAMD_diePKc+0x62 [0x500082]
> > [2] _ZN15GlobalMasterTcl10initializeEv+0x130 [0x789f22]
> > [3] _ZN15GlobalMasterTclC9Ev+0x66 [0x786426]
> > [4] _ZN15GlobalMasterTclC1Ev+0x6 [0x78646c]
> > [5] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x103 [0x56cb59]
> > [6] _ZN4Node7startupEv+0x287 [0x89f303]
> > [7] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x89f078]
> > [8] CkDeliverMessageFree+0x21 [0x9c2d71]
> > [9] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c2365]
> > [10] CsdScheduleForever+0xa5 [0xa4bcf5]
> > [11] CsdScheduler+0x1c [0xa4b8f6]
> > [12] _ZN7BackEnd7suspendEv+0xb [0x508add]
> > [13] _ZN9ScriptTcl9initcheckEv+0x80 [0x90041e]
> > [14] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x20 [0x8fccc4]
> > [15] TclInvokeStringCommand+0x91 [0xa6e208]
> > [16] /home/paulo/programas/NAMD/namd2 [0xaa4058]
> > [17] Tcl_EvalEx+0x176 [0xaa469b]
> > [18] Tcl_EvalFile+0x134 [0xa9c0a4]
> > [19] _ZN9ScriptTcl3runEPc+0x14 [0x8fc4e2]
> > [20] _Z18after_backend_initiPPc+0x22b [0x50481b]
> > [21] main+0x3a [0x5045ba]
> > [22] __libc_start_main+0xe6 [0x7ff1a10d4466]
> > [23] _ZNSt8ios_base4InitD1Ev+0x52 [0x4ff9ea]
> > Fatal error on PE 0> FATAL ERROR: expected integer but got "4240 4243"
> > while executing
> > "addatom $abf3"
> > (in namespace eval "::ABF::ABFcoord" script line 9)
> > invoked from within
> > "namespace eval ABFcoord {
> >
> > set abf1 $::ABF::abf1
> > set abf2 $::ABF::abf2
> > set abf3 $::ABF::abf3
> >
> > print "ABF> Using the abscissa of atom $abf3"
> >
> > adda..."
> > (procedure "ABFstartup" line 2)
> > invoked from within
> > "ABFstartup"
> > (in namespace eval "::ABF" script line 4)
> > invoked from within
> > "namespace eval ::ABF {
> >
> > # coordinate-specific startup procedure
> > ABFstartup
> >
> > if { [info exists restraintList] } {
> >
> > array set rArray $restraintList
> > ..."
> > (file "/home/paulo/Desktop/Tutorial-ABF/abf-1.8/abf_script.tcl" line
> > 766)
>
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