From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Jul 16 2014 - 10:46:48 CDT
As others have pointed out, there are now several resources scattered across the web for helping you obtain force field parameters for a molecule. Some of them work by analogy to molecules for which parameters are already available, others by fitting to first principles calculations, and some provide little more than Frankenstein's monster-type amalgams of parameters from various force fields and/or use derivation methods that are incongruent with the published standards for your target force field. If you are interested in obtaining high quality parameters, you should take care to understand the method the tool uses and whether it is appropriate for the force field employed in your simulations. The proper use of a parameterization tool and massaging the I/O into whatever form you need to make your MD run is really a secondary issue and is more appropriately directed to the authors and/or support systems for that particular program.
I am the author of the Force Field Toolkit (ffTK) distributed within VMD. To obtain parameters compatible with the CHARMM force field, I suggest obtaining initial parameters using the CGenFF Program (formerly Paramchem). This output will include penalty scores that will inform you which terms require additional testing and/or refinement, which can be done using ffTK.
If you are familiar with the CHARMM program, a good resource is:
But for that, of course, you would need very good knowledge of the CHARMM
program (you might even have to even obtain a copy of it which is not
On Tue, 15 Jul 2014, Abhishek TYAGI wrote:
> I want to run MD, but unfortunately I do not have the reasonable force field for this molecule.
> Now what I tried following approaches to get force field:
> 1. I tried CGenFF and got a *.str file but the data in the file is different from my input file i.e. mol2 file, the pdb format is different from the *.str file.
> 2. I tried to get force field from swissparam website and received the different file as *.par, *.top file, I tried MD on this field it runs successful, but the question is that is this correct approach?
> 3. I tried parameter tool available in VMD too I got some output from it too, but I am not able to connect all the information.
> Any guess what to do to get accurate force field parameter for the molecule
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