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Parametrizing ligand bound to lysine by Schiff Base
#38300 07/09/21 06:30 PM
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I am attempting to prepare the following PDB for simulation, and it features the ligand 5-OP-RU covalently bound to a Lys43 residue by a Schiff base. For reference, I obtained this file from RCSB 6PUF (chains C and F), and the ligand ID is 2LJ. I also modified the file to indicate that the bond between the lysine and ligand is a double rather than single bond.

I have attempted to upload my PDB to Ligand Reader and Modeler to parameterize the ligand, but there are a few errors in how the structure is read. 1) There are improper double bonds placed around the ring, and 2) The linking carbon of the Schiff base is given extra hydrogens that would prevent the covalent bond from forming. When I directly read in the 2LJ ligand ID into the program, the former issue is resolved but not the latter.

When I try to correct these mistakes on the structure, the website does produce parameter and topology files, but when I attempt to use them in conjunction with the PDB reader the website fails.

I would appreciate any advice on what my first steps should be.

Attached Files
MR1_5opru.txt (244.05 KB, 11 downloads)
SHA1: d020e5a9003031ad7e17bc957f5b9e678b226de7
Re: Parametrizing ligand bound to lysine by Schiff Base
Andrew, UChicago #38301 07/09/21 09:39 PM
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rmv Online Content
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Which web site are you referring to?

If it is charmm-gui, there is a forum for that here, but most questions posted go unanswered lately, as they prefer that people use the Contact page on the charmm-gui site.

Importing ligands which may or may not be be well defined in the CHARMM force fields can be an exercise fraught with peril. You should probably start with the CGenFF site; there are some useful posts in the Parameter forum, and a paper or two.


Rick Venable
computational chemist


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