VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Apr 06 2017 - 18:44:37 CDT

Dear Guanyu,

Regarding your Calcium atom, the calcium atom (and residue) name is CAL in
CHARMM topology and the atom or residue name in your pdb should match this
name. What did you mean by "binding to several residues"?

Regarding the carbohydrate residue, in fact autopsf automatically rename
NAG to BGLN. This is because pdb only assumes residue names containing up
to 4 characters, and as you can see from the top_all36_carb.rtf, there are
two GlcNAc residues, BGLCNA and BGLCN0 (original CHARMM topology names, not
VMD names). To use this "renaming" the user must provide the modified
topology file with the intend residue renamed as BGLN. A modified topology
file must be provided in the cases of residues containing more than 4
residues.

Best

Joao

On Thu, Apr 6, 2017 at 5:47 PM Guanyu Wang <wangg348_at_myumanitoba.ca> wrote:

> Hi there,
>
>
> I am new to VMD and I encountered some problems while using the Autopsf
> gui. My protein has a structural calcium binding to several residues. When
> I am trying to generate the psf file using Autopsf, the calcium ion is
> recognized as AO1. But in the final output, calcium is placed in the origin
> instead of where it should be. I was trying to patch the calcium ion to one
> of the residues. However, it gives the error message "psfgen) unknown
> patch type AO1:1". Is there any specific instructions I need to follow in
> order to include the calcium in the final output file? I would really
> appreciate it if someone could help me!
>
>
> And by the way, in the 1.9.3 Mac OS X X86 version of VMD, the topology
> file " top_all36_carb.rtf" renames NAG as BGLCNA. However, the "autopsf.tcl"
> renames NAG as BGLN. This causes autopsf to stop running because it cannot
> find BGLN in the topology file. This can be fixed by changing BGLCNA to
> BGLN in the topology file. I hope this can help someone with the same
> problem.
>
>
> Cura, ut valeas!
>
> Guanyu Wang
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380