Re: AutoPSF Error

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Mar 12 2018 - 12:22:35 CDT

Dear Alex,
Yes, you will need to either delete the residue with missing parameters, or
parameterize it and then try again. You could use the fftk plugin in vmd
for this purpose (be sure to read the paper and documentation thoroughly...
parameterization is usually a tricky business, although it looks like the
particular ligand that you have here could mostly be treated well with
cgenff parameters).
Best,
Peter

On Mon, Mar 12, 2018 at 11:40 AM, Alex Saad-Falcon <alexsaadfalcon_at_gmail.com
> wrote:

> Hello all,
>
> I would like to generate a PSF file for the protein with identifier 6CC0 (
> http://www.rcsb.org/structure/6CC0), but I am running into the issue
> where the ligand is unable to be parameterized. I am assuming it is because
> it is not part of any known amino acid or molecule in the parameter or
> topology file. How can I generate a psf for 6CC0, or can I get one from
> RCSB?
>
> Thanks,
>
> Alex
>

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