VMD-L Mailing List
From: kim, stephanie S. (kim.6088_at_buckeyemail.osu.edu)
Date: Thu Aug 04 2016 - 09:02:38 CDT
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Hi Joshua,
I've tried your suggestions, and after typing them in it said:
Info) 100.0% complete (frame 49999)
But nothing happened to my trajectory.
I've loaded the psf and dcd file and opened the TkConsole to type in pbc wrap commands. Am I doing this wrong?
If I do pbc wrap commands, will it overwrite the existing dcd file?
Thank you,
Stephanie
________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Wednesday, August 3, 2016 2:24:32 PM
To: kim, stephanie S.; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Aligning a dcd file of a protein consisting two chains
Hi Stephanie,
The way I like doing it is through two successive calls to pbctools.
pbc wrap -compound fragment -center com -centersel "chain A"
pbc wrap -compound fragment -center com -centersel "protein"
The idea behind these two commands is that the first will center is on one component of the protein. For most multimers, that will also put the other elements in the same box, and so you eliminate jumps that way. The second line then recenters it so that the protein as a whole is in the center of the box, not just one fragment. The second one could be replaced by another alignment script if you prefer.
-Josh Vermaas
On 08/03/2016 11:31 AM, kim, stephanie S. wrote:
Hello,
I've tried to align a trajectory of a protein consisting two chains, but when I load the aligned version of the trajectory, two chains separate, jump around for couple of frames and then would come back. A colleague suggested using ptraj commands: "center" and "image center familiar" instead, because he had the same problem before with aligning a trajectory consisting two subunits using vmd.
Can you suggest any other tcl scripts that would fix this problem? Or could you suggest a script that correlates to the ptraj command "center" and "image center familiar"?
I've used this script to align the trajectory:
______________________________________
proc align { rmolid smolid2 seltext } {
set ref [atomselect $rmolid $seltext frame 0]
set sel [atomselect $smolid2 $seltext]
set all [atomselect $smolid2 all]
set n [molinfo $smolid2 get numframes]
for { set i 1 } { $i < $n } { incr i } {
$sel frame $i
$all frame $i
$all move [measure fit $sel $ref]
}
$ref delete
$all delete
$sel delete
return
}
align 0 0 "protein"
______________________________________
Thank you,
Stephanie Kim
Graduate Student
Department of Chemistry and Biochemistry
The Ohio State University
2116 Newman & Wolfrom Laboratory
100 W. 18th Ave
Columbus, OH 43210
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