From: Smith, Harper E. (
Date: Wed May 19 2021 - 13:01:13 CDT

Hi Arthur,

Are you sure the parameters are not already available? If not, try ffTK


From: <> on behalf of Arthur Pereira da Fonseca <>
Sent: Wednesday, May 19, 2021 1:04 PM
To: <>
Subject: vmd-l: Generating parameter files


Iím trying to run a dynamic analysis using NAMD. First I generate a valid psf file using VMD. For the two actions I need a valid parameter file to work with my molecule. The problem is: I'm running a peptide, from pdb server, that contains engineered residues. That means I have to provide specific parameter files in order to run these.

So my question is: how can I generate these files?

I tried with CGenFF, but I got an error saying: "unfulfilled valence in aromatic subgraph". I also tried reading their FAQ and using the softwares they suggest to generate the mol2 files, but with no luck. I tried using SPARTAN, from the "Parameterizing a Novel Residue" tutorial. But, again, I found myself with an error.

So is there any other way to generate the needed files? Or something I can do to overcome these errors? I know it must be a problem with carbon valances within the peptide, but I donít have enough chemical knowledge to fix this. Anyway, I'm attaching my molecule to this message.

Any help is appreciated.