From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Mon Nov 28 2016 - 19:44:01 CST
Hi Jerome,
thanks a lot! ABF will be done in small enough windows, so there is no need
to tie the center of the sphere to the moving target ion, I think. I will
restrain the backbone of the protein to not let it drift.
Olga
On Mon, Nov 28, 2016 at 1:45 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Hi Olga,
>
> Right now you seem to be pushing ions away from a fixed position. That
> should be fine as long as that position is correct, that is unless the
> protein drifts away.
>
> If you were to use the position of the tagged ion instead, and apply ABF
> to that ion, then things would get more complicated because your restraint
> would introduce a coupling between the tagged ions and the others.
>
> Jerome
>
> On 28 November 2016 at 19:36, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
>> Hi all,
>>
>> I would appreciate if someone could comment on the script I made to push
>> ions away from the tagged ion during abf simulations inside the ion
>> channel. It seems to work the way it is now for simple equilibration, but I
>> am not sure whether this is correct, especially when combined with SMD
>> and/or ABF. If I apply force to the tagged ion, can it interfere somehow
>> with the tclBC that I apply to surrounding ions?
>>
>> The simulation system is a protein channel solvated in NaCl and the
>> permeating (tagged) ion is sodium with a known atom id number (344742,
>> obtained by get serial command in VMD). I want to push all ions away from
>> the tagged ion and leave the protein unaffected. For that I distinguish
>> ions from the protein's atoms by mass. The sphere radius and the force
>> strength are set in the main configuration file. Here is a tclBC scrpt that
>> is called from within the main configuration file:
>>
>> #Set a list of atom IDs of all the ions
>>
>> set ionList {}
>> set atomID 1
>> set inStream [open $pdbSource r]
>> set sphereCenter {22.5 89.6 93.2} ; #this is the position of the tagged
>> ion
>>
>> # go through pdb file and find entries for ions and save them to the list
>>
>> foreach line [split [read $inStream] \n] {
>>
>> set string1 [string range $line 0 3]
>> set string2 [string range $line 17 20]
>> set string2 [string trim $string2]
>>
>> if { [string equal $string1 {ATOM}] || \
>> [string equal $string1 {HETA}] } {
>>
>> if { [string equal $string2 {CLA}] || \
>> [string equal $string2 {SOD}] } {
>> lappend ionList $atomID
>> }
>>
>> incr atomID
>> }
>> }
>> close $inStream
>>
>> wrapmode cell
>>
>> proc calcforces {step unique} {
>>
>> global atomID sphereCenter sphereRadius maxForce ionList
>>
>> # find the components of the sphere's center
>>
>> foreach { x0 y0 z0 } $sphereCenter { break }
>>
>> while {[nextatom]} {
>>
>> set atomid [getid] ;# get the ID of the current atom
>>
>> # check if this ID is listed in ionList
>>
>> if { [lsearch $ionList $atomid] >= 0 } {
>>
>> set rvec [getcoord] ;# get ion's coordinates
>> foreach { x y z } $rvec { break }
>>
>> # get distance between the ion and the sphere's center
>>
>> set rho [expr sqrt(($x-$x0)*($x-$x0) + ($y-$y0)*($y-$y0) + \
>> ($z-$z0)*($z-$z0))]
>>
>> if { $atomid == 344742 || [getmass] < 22 || [getmass] > 36 } {
>> dropatom
>> continue
>>
>> } else {
>>
>> set forceX [expr $maxForce * ($x-$x0) / $rho]
>> set forceY [expr $maxForce * ($y-$y0) / $rho]
>> set forceZ [expr $maxForce * ($z-$z0) / $rho]
>> }
>>
>> addforce "$forceX $forceY $forceZ"
>> }
>> }
>> }
>>
>> Does it look correct? I would very much appreciate your comments! Thanks
>> in advance,
>>
>> Olga
>>
>
>
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