How to perform a MDs of a phosphorylated protein

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GROMACS version:
GROMACS modification: No

Hello everyone…
I’m interested in performing a simulation with the AMBER99SB-ILDN force field, but I need to phosphorylate certain residues in the protein.

However, I haven’t found the steps to obtain a pdb or gro file with the phosphorylated protein and residues.

If anyone could direct me to a tutorial or share the steps for phosphorylation…

Any information would be greatly appreciated in advance.

2

The structure part is usually simple - you can just copy/edit the atoms manually in VMD. You’ll need to choose the protonation states, that can depend on your local environment or target pH.

(If that’s too cumbersome for multiple modifications, I could still try to add a quick function to phosphorylate a residue in a structure; wouldn’t be too hard in the end. I see someone mentioning Chimera has this functionality though.)

For topology, Amber has official templates for phosphorylated AAs in .../dat/leap/cmd/leaprc.phosaa10 - if you have ambertools installed, you can convert this file to .rtp templates and extra bonded/nonbonded terms following this tutorial:

In my case, it was as easy as

import gromologist as gml
gml.amber2gmxFF('.../dat/leap/cmd/leaprc.phosaa10', 'pho.ff')

and then merging files from pho.ff into your FF files.

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