Dear all,
I have been trying to "wrap" my protein in the trajectory using the following command, using VMD:
set sel [atomselect top protein]
pbc wrap -centersel $sel origin -compound res -all.
I am not sure if it works, because even though I can see how it process the frames, all atoms appear in white and proteins does not move at all.
Also, when I try to save my trajectory by using:
anímate write dcd new.dcd sel $sel my trajectory is not saved
Do you have any recommendation? I would really appreciate them.
Thanks in advance.
Dear Marlet, first the cell dimensions must be read from the xst file. For example:
package require pbctools
mol load psf run.psf dcd res0.dcd
pbc readxst res1.xst -molid top -all
Dear Marlet, first the cell dimensions must be read from the xst file. For example:
package require pbctools
mol load psf run.psf dcd res0.dcd
pbc readxst res1.xst -molid top -all
to wrap:
pbc -wrap -all -compound res -center bb -centersel "protein"
to write dcd:
animate write dcd my.dcd
Ramin Ekhteiari Salmas will pbc -wrap -all -compound res -center bb -centersel "protein" include the metal ions in the structure ?
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