I am a beginner in the field of molecular dynamics and biochemistry. I need the parameters such as van der Waal radii, partial charge of each amino acid. How do I read directly the parameters from the online database if there exists any?
For the CHARMM36 force field, you can follow this link -
https://www.charmm.org/charmm/resources/charmm-force-fields/
Parameters used in Gromacs - (Amber, OPLS, CHARMM22, GROMOS, etc.)
http://www.gromacs.org/Downloads/User_contributions/Force_fields
A good discussion about the development and implementation of forcefield can be found here - https://ambermd.org/AmberModels.php
Depending on the Forcefield(FF) that you are looking at I would always suggest you find the original study that published the FF parameters and where they have come from to get a good understand on their limitations.
Thanks Alexandru Moldovan and Suparna Ghosh . In AMBER folders, I am able to read partial charge values on all amino acids. But I still have some issues like, for N terminus amino acid, I need NH_2 at the N terminus, However, they have given partial charges for N terminus amino acid with NH_3+. I am not able to see anything like that in the AMBER folders. Where do I find partial charges of amino acid with NH_2 terminus amino acid? The same happens for C terminus, AMBER folder shows only the files containing C terminus amino acid with COO- end instead of COOH
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