I began to run a MD simulation using the GROMACS program. In the first step, pdb2gmx, it was asked to select the force filed. How do I select the right force field?
I do have similar question but I get error as file input/output error. Any help??
OPLSAA will serve for all atoms of protein. For ligand u must use same forcefield for generating its parameter and toplogy file. Search gmx userlist for answers. You will get lots of suggestion. http://www.gromacs.org/Support/Mailing_Lists/Search
For protein ligand system you can use either amber fiels ff99SB or newer ff99SB-ildn which takes care of side chain as well. But for ligand it is difficult to make the topology in gromacs you can use some online servers or make the topology using amber tools which is free and convert through acpype which is free and easy as well. hope this helps
Please note, that automagically generated parameters most substances should be treated with caution.
In many cases you can't simply generate it & simply use - they're rather suggestions that should be refined.
If your ligand is so specific that you can't find parameters I'd suggest preparing them "by hand". There are tutorials explaining this process, like for example (in CHARMM ff case) this one (warning! very basic, but clarifies the idea):
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/
Good luck!
I prefer GROMACS as it is flexible, while you work with CHARMM your calculaton time would be large compared to GROMACS or AMBER.
Mr Stéphane Abel have given detailed and very good reply, super like.
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