Dear all,
I am running MD simulation of a protein containing a zinc finger (ZnF) domain. I got its all-atom pdb file and I know there are 4 sulfur atoms in 4 cycteins of ZnF domain interacting with the zinc.
I want to add a zinc to the position near the ZnF domain (edit pdb file?) and then I will sovalte it via Gromacs, and then convert it to Amber files and run the final MD on Amber.
Or should I add zinc after I convert files to Amber files, like edit the parm7 file?
Or adding zinc after Gromacs or during Gromacs but before Amber?
Which way would be better and how can I do? Thanks.
Add protein + zinc and then solvate the protein ligand system.
use pymol for editing pdb file.
https://codeyarns.com/tech/2013-05-12-how-to-move-one-molecule-in-pymol.html#gsc.tab=0
I just try to edit the pdb, adding a zinc near the ZnF domain, and then use VMD to move zinc to the position near the ZnF binding position.
Then I use Gromacs to perform energy minimization and equilibration.
I check the final gro output file and it shows zinc still in the ZnF binding pocket.
So I think this way works?
Is there anything I missed?
Eventually, I use Modeller to combine the full length pdb with experimental ZnF domain structure pdb, which containing zinc, then do the following simulation.
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