VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon May 21 2018 - 09:57:49 CDT

Hi Kelly,

The reason why you are not seeing the new residue in the table when adding
the new topology is that your new residue has the same name of the protein
residue Methionine (MET). As a safety measure, QwikMD ignores the residues
already defined in the topology files loaded in its database, which in this
case is declared in the protein residues topology file.

One should be careful in naming novel residues and its atoms, as it can
create conflicts with the already existing defined residues.

Best

João

On Thu, May 17, 2018 at 12:40 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I went through the FFTK tutorial to parameterize a drug molecule, but when
> I use VMD -> QwikMD -> load the protein pdb with drug in it, and
>
> then structure manipulation -> add topo+param -> +, and then select my
> .str file for the drug, nothing happens. Nothing appears in the window/list
>
> for Topology & Parameters Selection. I attached my .str file here. What
> am I missing? Thanks!
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851