I have looked through some papers and also on Jorgensen's website, but i cant find parameters for all elements. They also have a web server where you can upload a structure and it will spit out constants for different interactions. But it doesn't give diherdral coefficients for all bond types. If this doesnt work then i'll probably use UFF.
Unfortunately, OPLS parameters (and parameters in many other force fields) are not easy to obtain, even from the papers that claim to include them. It is sometimes possible to obtain them by rigorous searching in many papers and associated documents, but that does not happen often. Also, if I'm understanding your question correctly, you're probably going to have a difficult time finding parameters for obscure atom types; OPLS includes only a few elements that aren't immediately relevant in biophysical simulations.
I'm aware of a few options, but there are probably more:
1. GROMACS ships with a few force fields, including OPLS. There are often found in a folder like /usr/local/gromacs/share/gromacs/top/oplsaa.ff/. There are a few typos, but it includes most parameters and is probably mostly accurate. If you wanted to transfer a system to and from GROMACS and another simulation engine like LAMMPS, you could use ParmEd or Intermol.
2. Our group has developed a tool named foyer that atomtypes systems. It currently supports a large portion of the OPLS force field. It is designed to be as general and easy to use as possible, requiring only a coordinate file and force field file (in the case of OPLS, this is provided within foyer). You can see more at https://github.com/mosdef-hub/foyer
3. Derive your own parameters. Definitely the hardest option of the three...
Also, I don't know what system you're studying, but UFF is rarely sufficient to describe interesting systems. It's useful as a starting point or if there are literally no other parameters, but it should be avoided if possible.
Unfortunately, OPLS parameters (and parameters in many other force fields) are not easy to obtain, even from the papers that claim to include them. It is sometimes possible to obtain them by rigorous searching in many papers and associated documents, but that does not happen often. Also, if I'm understanding your question correctly, you're probably going to have a difficult time finding parameters for obscure atom types; OPLS includes only a few elements that aren't immediately relevant in biophysical simulations.
I'm aware of a few options, but there are probably more:
1. GROMACS ships with a few force fields, including OPLS. There are often found in a folder like /usr/local/gromacs/share/gromacs/top/oplsaa.ff/. There are a few typos, but it includes most parameters and is probably mostly accurate. If you wanted to transfer a system to and from GROMACS and another simulation engine like LAMMPS, you could use ParmEd or Intermol.
2. Our group has developed a tool named foyer that atomtypes systems. It currently supports a large portion of the OPLS force field. It is designed to be as general and easy to use as possible, requiring only a coordinate file and force field file (in the case of OPLS, this is provided within foyer). You can see more at https://github.com/mosdef-hub/foyer
3. Derive your own parameters. Definitely the hardest option of the three...
Also, I don't know what system you're studying, but UFF is rarely sufficient to describe interesting systems. It's useful as a starting point or if there are literally no other parameters, but it should be avoided if possible.
Thanks for the answer, I'll check out foyer. I want to look at a silica cluster which has been terminated by fluorine atoms. I have attached a pdb file of the structure.
Hello, you can use: http://erg.biophys.msu.ru/tpp/
is a free web-service, TPPMKOP is an utility developed for the automatic topology generation working well with OPLS-AA force field.
It doesnt recognize all atoms in the structure and I get the following error-
Your molecule have atoms in unrecognized chemical environment.
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