I recently completed an MD simulation of a protein-ligand complex using Amber, and everything appeared to run without any errors. However, when I converted the trajectory file (.nc) into a .pdb file using CPPTRAJ, I encountered an issue where some of the water coordinates are missing and are represented as ****** in the resulting .pdb file. I needed the coordinates since I am interested in studying the local structure of hydration water around the protein. I am wondering whether the issue could be due to the conversion process or if it might be related to the MD simulation itself. Any insights or suggestions on how to resolve this issue would be highly appreciated.
Let's say you have Amber run trajectory(#.nc) and prmtop (#.prmtop) files, then you can make pdb for each frame from your traectory using these commands in cpptraj=====>(It should contain all the atoms present in your trajectory including waters, unless you strip them)
#=====cpptraj commands======
parm #.prmtop
trajin #.nc
trajout frame.pdb pdb multi run
#==========================
Thank you so much for your response. I did the way you have mentioned but missed including the keyword 'autoimage’ due to which coordinates of some water molecules were missing. Autoimage automatically center and image a trajectory with periodic boundaries.
Yes, if you have any image effect in your trajectory you can use this commands====>
#=====cpptraj commands======
parm #.prmtop
trajin #.nc
autoimage
center :1-10 mass origin # (lets 1-10 is the resid of protein ligand complex, it will center them)
image origin center
trajout frame.pdb pdb multi run
#==========================
Hope this will work without showing any error.
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