GROMACS version: 2018.3
GROMACS modification: No
I am running MD simulation for a protein.
A simulation box was created, and the protein was solvated. But when I used Amber99SB-ILDN, side chain of C-terminus residue seems detached and doesn’t appear as a part of the protein on VMD.
But the structure looks fine when I use Gromos54a7. Has anyone experienced this kind of issue?
Thank you.
The protein is fine, see http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc
Plus could also be due to VMD not knowing which bonds should be there, it guesses based on distance, see http://manual.gromacs.org/documentation/current/user-guide/faq.html#analysis-and-visualization
Thank you for the reply. I guess I will just try moving onto the next step, and see if something weird happens.
Another question has to do with creating .itp file for my ligand.
I use ATB web server to create one for Gromos forcefield, but not sure about what to use for Amber99SB-ILDN. I found that I should use acpype, but not quite sure how to set it up and use it. Some links to the tutorial do not exist anymore.
Any help will be appreciated.