VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Tue May 26 2020 - 09:50:12 CDT

Whats the residue name in the topology files CHARMM-GUI provided, and does
it match what is in the input structure? That is how psfgen/autopsf does
the matching, and if that is incorrect, Autopsf will ignore the parts that
aren't parameterized. I'm not entirely sure how the molefacture part screws
around with this, but I've always done it the old-fashioned patching way.
-Josh

On Tue, May 26, 2020 at 8:31 AM Hélder Bandarra Tavares <
H.D.BandarraTavares_at_tudelft.nl> wrote:

> I'm trying to bind a molecule (mostly composed of PEG chains) to
> Hemolysin. I have the .pdb and .psf files of both. To do so, I placed the
> molecule close to the residue I want to link it to and created a bond using
> Molefacture, and now I wanted to generate a .psf file to run a MD
> minimization/equilibration afterwards with NAMD. However, using Autopsf I
> get the following message: "Autopsf has detected 1 unparametrized
> components", and this component is the molecule I want to link. It is worth
> noting that that molecule has no non-standard atoms and that I loaded the
> topology files provided by CHARMM-GUI for this molecule.
>
>
> What can I do to generate the .psf file? Is there other way to do so?
>
>
> Thank you in advance,
>
> Hélder Tavares
>
>
>
>