GROMACS version: 2022.1
GROMACS modification: No
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Hello for the above topic my Pymol minimization visualization of my membrane-heptamer is compressed only exhibiting a monomer, is this result correct or should I rerun? (See screenshot.)
Thanks:) Joelđź’ˇ
Looks like everything is squished inside a box that is much too small for the contents of the system.
HI Justin thank you for your kind update and yes I agree.
I input the below Minimization Script subsequent to CHARMM protein membrane implantation:
Below is the README Script prior to my above amendment
Below is the Gromacs Folder Results generated subsequent to the CHARMM protein membrane implant:
I believe I amended the README minimization script accordingly but do not know why my result is compressed and only a monomer from the heptamer. If you have any suggestions please let me know thanks:)
You shouldn’t change anything in the script that CHARMM-GUI gave you, and the contents of your first image (please use embedded text rather than screenshots) are not even syntactically valid.
The boilerplate CHARMM-GUI script is not diagnostic of anything; everyone gets this file.
Look at every coordinate file, including those from steps 1-5 during the build phases, to make sure you have what you think you do. The minimization procedure only acts on what is present, and in your original image, I see a few lipids, a big protein complex, and a few water molecules and ions. I suspect you didn’t build something correctly, even if the procedure “works” and lets you move forward.
Hi Justin thank you so much for your kind and prompt update and ok to all:).
Yes I inspected visually my protein-membrane system after each CHARMM step and the images were all satisfactorily represented, below is a screenshot of the satisfactory final model before the Gromacs minimization step that generated the failed compressed model, accordingly I will follow your instructions towards the CHARM-GUI Script, Best, Joel :)
