VMD-L Mailing List

From: Arthur Pereira da Fonseca (arthurpfonseca3k_at_hotmail.com)
Date: Wed May 19 2021 - 12:04:33 CDT

Hello,

I’m 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 don’t have enough chemical knowledge to fix this. Anyway, I'm attaching my molecule to this message.

Any help is appreciated.
Thanks!
Arthur