Re: Doubts and problem in ABF simulations

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Aug 31 2009 - 17:18:52 CDT

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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