From: João Ribeiro (
Date: Thu Apr 06 2017 - 19:13:34 CDT

Dear Guanyu,

please keep the vmd-l email in the conversation.

I would first fix the issue with the calcium atoms' name. Regarding the
coordination of the Calcium atoms, I would not be of much help. I know that
calcium atoms are tricky to simulate. Maybe another user used to work with
calcium might help you. I just wanted to clarify some confusion with
autopsf and topology files.

Best wishes

On Thu, Apr 6, 2017 at 6:57 PM Guanyu Wang <> wrote:

> Hi João,
> I am sorry for the ambiguity. I meant that the calcium ion is coordinating
> with several amino acids residues at a specific location. However, after
> running the autopsf, instead of staying where it should be, the ion is
> placed at (0,0,0) in the output pdb file. So I am wondering if there is
> anyway I can fix it? Thank you very much!
> Sent using OWA for iPhone
> ------------------------------
> *From:* João Ribeiro <>
> *Sent:* Thursday, April 6, 2017 6:44:37 PM
> *To:* Guanyu Wang;
> *Subject:* Re: vmd-l: Problems of generating the psf file with a protein
> that has a structural calcium
> 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 <>
> 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
> +1 (217) 3000380 <(217)%20300-0380>

João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3000380