VMD-L Mailing List

From: Hélder Bandarra Tavares (H.D.BandarraTavares_at_tudelft.nl)
Date: Tue May 26 2020 - 10:14:44 CDT

Dear Josh,

I assume the name in the topology file is "lig", as this is written in the file: "RESI lig -1.000 ! param penalty= 543.000 ; charge penalty= 289.749". I'm not sure where to see the name in the input structure, but the resname of the chain is LIG, as displayed in VMD. Does it match or is it case sensitive? I think it should be the same as I used the files given by CHARMM-GUI without changing them.

Thank you in advance,

Hélder Tavares

________________________________
From: Josh Vermaas <joshua.vermaas_at_gmail.com>
Sent: 26 May 2020 16:50:12
To: Hélder Bandarra Tavares
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Issues generating a .psf file

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<mailto: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