VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Mon Jun 27 2022 - 11:21:34 CDT

Quick solution is to always open the PDB produced by martinize.py before
loading any trajectory.
Make sure you need to remove the TER line, so VMD will use the CONECT
records to draw bonds.

ATOM 928 CA GLY B 275 -14.986 31.558 26.549 1.00 0.00

*TER 929 GLY B 275*CONECT 1 2 3

You may write a simple script to write only the bonds from selected atoms,
for a cleaner look.
Here are two scripts, "Script 1" to write the bond list, you only do this
once. Script 2, to read it anytime you need.

# Script 1: Write a martini bond list for Backbone atoms, from PDB file.
#1 Open the PDB file
  mol new *martini.pdb*
#2 Select
  set BB [atomselect top "name BB"]
#3 Get bonds
  set bondlist [ $BB getbonds ]
#4
  set f [open "*bondlist.dat*" "w"]
  puts $f $bondlist
  close $f

# Script 2: Read bond list
#1 Read bondlist file
  set f [open "*bondlist.dat*"]
  set bondlist [read $f]
  close $f
# 2 Create a selection to apply bond list
  set BB [atomselect top "name BB"]
# 3 Set bonds to selection
  $BB setbonds $bondlist

On Mon, Jun 27, 2022 at 8:36 AM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> If you implicitly trust what is in the tpr file, and don’t mind
> recompiling VMD, there is also https://urldefense.com/v3/__https://github.com/jvermaas/vmd-tprreader__;!!DZ3fjg!4kzve3owgnOQLiDBysN2cFKWCJWNC5wAJ8SR9QjMuQF8F082mXj7Lg8FSh5QssfbWMEbyYkTlscLZumY66Yo$
> <https://urldefense.com/v3/__https://github.com/jvermaas/vmd-tprreader__;!!DZ3fjg!7aSXUbrIw_xov2Ovb09kW90HuPo0Drna3fAi21D4UaxzHtzI0BQS5e_mgbhct5MYpQxwr9Ov5nRGRKW3wBk$>,
> which will read the definitions from the tpr file. I have not checked if
> GROMACS 2022 changed the tpr generator (again) or not in a way that breaks
> the tpr reader.
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of "Smith, Harper E." <
> smith.12510_at_buckeyemail.osu.edu>
> *Date: *Sunday, June 26, 2022 at 7:58 PM
> *To: *Raman Preet Singh <ramanpreetsingh_at_hotmail.com>, "vmd-l_at_ks.uiuc.edu"
> <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: Re: Visualisation of CG bonds
>
>
>
> Hi Raman,
>
>
>
> You can use the "DynamicBonds" representation in VMD and change the
> distance cutoff.
>
>
>
> HTH,
>
> Harper
> ------------------------------
>
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
> *Sent:* Sunday, June 26, 2022 2:07 PM
> *To:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* vmd-l: Visualisation of CG bonds
>
>
>
> Dear All, I have run a CG simulation in Gromacs using Martini FF and would
> like to visualise the trajectory in VMD. There's a Tcl script available on
> Martini website but that keeps on returning errors (with both, the .tpr
> file and the .top
>
> Dear All,
>
>
>
> I have run a CG simulation in Gromacs using Martini FF and would like to
> visualise the trajectory in VMD. There's a Tcl script available on Martini
> website but that keeps on returning errors (with both, the .tpr file and
> the .top file). The errors have been reported by others also but the fixed
> used by others have not worked in my case.
>
>
>
> As I understand,VMD draws bonds based on a distance based cutoff. I was
> wondering if there is a way to draw long bonds, as is typical in CG MD, in
> VMD. In case VMD can not do that, is there any other visualiser that can be
> of help.
>
>
>
> Regards,
>
> Raman
>
>
>
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics
Leach Science Center
Auburn University
dgomes_at_auburn.edu
+1 (334) 559-4016