sir I have attached the files below and I want to pull the ligand from -y axis becz it shows important interactions towards that side.
(Attachment newbox.txt.gro is missing)
image is not clear, zoom out and show the system , looks like you need to rotate the whole system that it aligns to the positive y axis, that makes everything easy.
sir how can i align this system , can u please tell.
I have sent you 3 file in your email, please update the status here so that community can get benefit @Manish
Thank you so much sir for your quick guidance. I wanted to ask if you changed anything in the structure, if yes what is it and how did you do it. Also do we need to change anything in the pull.mdp file.
i have rotated the whole structure towards particular axis- so that it is easy to pull. check the orientation and select the direction you wanted to pull.
Thank you sir, canyou please tell by what source or technique you rotated the whole structure towards a particular axis, so that i could use it in future.
pymol
ok sir i will also try to do the same with other proteins. Thank you so much sir.
sir, please can you tell the commands you followed in pymol to set the axis of protein for proper alignment, as I am unable to do it.