My protein source file (pdb) contains FE2+ (co-factor) and 2-oxoglutarate (co-substrate) but none of the force fields can incorporate them in while giving for MD simulation.
Dear Charles
First options: If FE2+ is not found in a topology database you can add necessary parameters manually. Look for papers maybe somebody has already used it in simulation.
Second option: You can use online servers that generates topology such as https://atb.uq.edu.au/ , http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg , http://www.aribeiro.net.br/mktop
Dear Charles
First options: If FE2+ is not found in a topology database you can add necessary parameters manually. Look for papers maybe somebody has already used it in simulation.
Second option: You can use online servers that generates topology such as https://atb.uq.edu.au/ , http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg , http://www.aribeiro.net.br/mktop
Add your parameter in topology fiels,refer unit five of the manual respective itp,atp files you have add
Hi Davis,
You can get the coordinates of 2-oxoglutarate from the popular online servers based on your force-field selection, and add them in *.gro file and *.top file (using include mechanism) after processing the topology through pdb2gmx.
But the problem is about "Fe+2", and i am hoping that i would be in coordinate-covalently bonded to the cosubstrate/protein. Simulation of coordinated bonds is challenging, and you need to be careful of how you treat this particular bond. A few options that I have read is to fix the Fe at the place (not very good option), or fix the distance of Fe from interacting atoms.
Finally, although, I did not perform myself but I read regarding atomic bond breaking/formation. You can simulation that particular region (Fe+2 and atoms close to it) as per Quantum Mechanics definition to replicate the biological phenomenon. It is hard but still possible in GROMACS.
Good uck,
Ayaz
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