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How is it possible to calculate a distance between a water...
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+ Mass
+ Molecular dynamics
+ Atoms
+ Molecular structure
+ Water
+ Pdb
Posted by
Leobert Samarita
How is it possible to calculate a distance between a water...
Hey Stefania, I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
Hey Stefania, I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
Hey Stefania, I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
Hey Stefania, I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
To add to Davide's answer: I would recommend using the collective variables plugin of VMD. The "distance" collective variable will measure the COM distance between two groups; you can define the water molecule as one and the other atoms of interest as the other group. The advantage of this method is that you can indicate whether you want the absolute distance or the shortest distance (if periodic boundaries were used). General information for running the VMD colvars module can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node211.html and more info on the distance colvar can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node227.html#SECTION001641100000000000000
To add to Davide's answer: I would recommend using the collective variables plugin of VMD. The "distance" collective variable will measure the COM distance between two groups; you can define the water molecule as one and the other atoms of interest as the other group. The advantage of this method is that you can indicate whether you want the absolute distance or the shortest distance (if periodic boundaries were used). General information for running the VMD colvars module can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node211.html and more info on the distance colvar can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node227.html#SECTION001641100000000000000
Hey Stefania,
I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
Hey Stefania,
I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
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Hey Stefania,
I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
Hey Stefania,
I would write a simple tcl script that can be launched in VMD http://www.ks.uiuc.edu/Research/vmd/ (or with VMD by giving the -dispdev text command) while you load a PDB file. If I correctly understand your problem, I would load the file select the water molecule(s) of interest and then measure the distance of those atoms (you can easily pick the atoms that are within a cutoff from any selection (in your case a water molecule) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node17.html). You can iterate through the collected frames of the trajectory and then write this distance in a text file that you can plot using a plotting software (command to measure distance using vmd: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html). Once you have the script you should be able to launch it while you load your coordinates and trajectory using VMD. Something like this: vmd COORDINATE TRAJECTORY -dispdev text < YOURSCRIPT.tcl Hope this helps, Cheers, Davide.
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To add to Davide's answer: I would recommend using the collective variables plugin of VMD. The "distance" collective variable will measure the COM distance between two groups; you can define the water molecule as one and the other atoms of interest as the other group. The advantage of this method is that you can indicate whether you want the absolute distance or the shortest distance (if periodic boundaries were used). General information for running the VMD colvars module can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node211.html and more info on the distance colvar can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node227.html#SECTION001641100000000000000
To add to Davide's answer: I would recommend using the collective variables plugin of VMD. The "distance" collective variable will measure the COM distance between two groups; you can define the water molecule as one and the other atoms of interest as the other group. The advantage of this method is that you can indicate whether you want the absolute distance or the shortest distance (if periodic boundaries were used). General information for running the VMD colvars module can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node211.html and more info on the distance colvar can be found here: http://www.ks.uiuc.edu/Research/vmd/current/ug/node227.html#SECTION001641100000000000000
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Use VMD for such calculation, you can use following script
Use VMD for such calculation, you can use following script
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hi dear Stefania
I think it helps you
good luck
https://hal.archives-ouvertes.fr/jpa-00253718/document
https://www.mysciencework.com/publication/read/1580471/the-druggable-antimalarial-target-1-deoxy-d-xylulose-5-phosphate-reductoisomerase-purfication-kinetic-characterization-and-inhib
hi dear Stefania
I think it helps you
good luck
https://hal.archives-ouvertes.fr/jpa-00253718/document
https://www.mysciencework.com/publication/read/1580471/the-druggable-antimalarial-target-1-deoxy-d-xylulose-5-phosphate-reductoisomerase-purfication-kinetic-characterization-and-inhib
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