VMD-L Mailing List

From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Wed May 19 2021 - 13:01:13 CDT

Hi Arthur,

Are you sure the parameters are not already available? If not, try ffTK https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf

HTH,
Harper

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Arthur Pereira da Fonseca <arthurpfonseca3k_at_hotmail.com>
Sent: Wednesday, May 19, 2021 1:04 PM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Generating parameter files

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