Re: Any NAMD-Working Small Organic Molecule

From: Gumbart, JC (
Date: Mon Mar 11 2019 - 23:57:11 CDT

Hi Alex,

Why not take pyrrolidine from the FFTK tutorial? Or you need it to be bigger? We’ve also done macrolides and cobalamins in our published papers, but these are bigger than 50 atoms.

There are a ton of other organic molecules in the CGenFF force field, but probably none quite that big.


> On Mar 11, 2019, at 8:35 PM, Alex Saad-Falcon <> wrote:
> Can anyone please send me a small organic molecule they have developed parameters for? It can be literally any small organic molecule (~50 atoms or so), and I need the .pdb, .psf, and .par files for it (topology not necessary if psf is provided)
> I need to get simulations running soon, so please send if you have one.
> Thanks,
> Alex

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