cg_bonds.tcl script

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Kargar
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12 years 10 months ago #705 by Kargar

cg_bonds.tcl script was created by Kargar

Dear All,

Thank you very much for cg_bonds.tcl script. I used it but I think I am making mistakes some where. Here it is the way I used to visualize:
1. open VMD
2. load .gro file e.g. 8-I-100ns-water.gro
3. open TKConsole
4. In TKConsole, "source cg_bonds.tcl"
5. cg_bonds -gmx /usr/local/bin/gmxdump -tpr 8-I-100ns-water.tpr

Type of topology detected: Martini (if this is wrong, you can precise the good one with the '-ttype' option).

# Molecule ID Number of Occurence Martini bonds & ElNeDyn Index of
name atoms constraints bonds first atom
--

0 Protein 0 56 1 44 16 8 0 0
1 W 1 1 994 0 0 0 0 56
2 Protein 0 56 1 44 16 8 0 1050
3 W 1 1 994 0 0 0 0 1106
4 Protein 0 56 1 44 16 8 0 2100
5 W 1 1 994 0 0 0 0 2156
6 Protein 0 56 1 44 16 8 0 3150
7 W 1 1 994 0 0 0 0 3206
8 Protein 0 56 1 44 16 8 0 4200
9 W 1 1 994 0 0 0 0 4256
10 Protein 0 56 1 44 16 8 0 5250
11 W 1 1 994 0 0 0 0 5306
12 Protein 0 56 1 44 16 8 0 6300
13 W 1 1 994 0 0 0 0 6356
14 Protein 0 56 1 44 16 8 0 7350
15 W 1 1 994 0 0 0 0 7406
--

bb-bb bb-sc sc-sc bb-bb

Here I expect my proteins with bonds, but without any changes. Please help me:(
To visualize the trajectory file, I think we should load .trr or .xtc file as a data to .gro file. Am I right?
Thank you very much

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Clement
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12 years 10 months ago #706 by Clement

Replied by Clement on topic cg_bonds.tcl script

Hi Kargar,

According to the table, the script did its work - parsing the .tpr and finding the bonds and constraints. I don't really understand why they're not drawn; I would need a little more details here! But I can give you the solutions of two issues (related to yours) people have with this script:

The cutoff to draw the bonds is too small (7 angstroms, used to avoid bonds crossing the entire simulation box); you can increase it via the -cutoff option.[/ol]

The beads you ask VMD to draw are not the good ones; to see the bonds, the beads involved in these bonds have to be part of a VMD representation (by default, you need a representation all, or at least name "B.*" for the backbone).[/ol]To answer your second question: to visualize your trajectory, you need to load an .xtc or .trr file on top of your molecule (use the Load Data Into Molecule menu of VMD).

Hope it helped; let me know if it works...
Clement

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Kargar
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12 years 10 months ago #707 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

Hi Clement

Thank you for your reply. I examined to ways you mentioned: I increased cutoff to 30 angstroms, but no results. In VMD >Graphical Representations, I used CPK for style, Name for color, name "B.*" and all for selection, but without any results. Please guide me.

Thank you in advance

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Clement
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12 years 10 months ago #708 by Clement

Replied by Clement on topic cg_bonds.tcl script

Humm... Ok. It will be simpler if I can take a look to the files directly. Could you send them to This email address is being protected from spambots. You need JavaScript enabled to view it.? I would need a .gro and .tpr, both of them describing the same system of course. I'll try to understand why it's not working and fix the script if needed...

Anyway, thanks for the feedback! May result in the correction of some bugs.

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Clement
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12 years 10 months ago #709 by Clement

Replied by Clement on topic cg_bonds.tcl script

Works perfectly for me!

I followed the same steps as you (loading the .gro, sourcing the script downloaded from the martini website, run cg_bonds -gmx /path/to/my/gmxdump -tpr 8-I-100ns-water.tpr without changing the cutoff), and the same representations (name "B.*" to show the backbone, all to show the rest of the system). The table given in output is the same as the one you posted a few days ago.

I'm still trying to figure out where you're problem is coming from...

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Kargar
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12 years 10 months ago #710 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

Hi Clement

I examined the script on other systems, but without any results.
Thank you very much for your attempt. I am looking forward hearing from you.

Kargar

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xavier
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12 years 10 months ago #711 by xavier

Replied by xavier on topic cg_bonds.tcl script

Dear Kargar,

I think Clement has given you all the answers you need already and most likely there is nothing wrong with your system or with the script.

You need to play with VMD graphics representation to visualize the system. The script does not produce any representation by default. It is up to you to choose how to represent the system.
You can try the licorice representation on all the backbone beads ("B.*") or any other selection of atoms ... it is up to you.

Kargar wrote: Hi Clement

I examined the script on other systems, but without any results.
Thank you very much for your attempt. I am looking forward hearing from you.

Kargar

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Clement
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12 years 10 months ago #712 by Clement

Replied by Clement on topic cg_bonds.tcl script

Kargar, here is what you need to do. First, go to the directory where your .gro and .tpr files are; then:

kargar@machine $ vmd 8-I-100ns-water.gro
vmd > source /home/where/is/your/cg_bonds.tcl
vmd > cg_bonds -gmx /where/is/your/gmxdump -tpr 8-I-100ns-water.tpr

The few lines above will:

load the 8-I-100ns-water.gro conformation;
source the script;
draw the martini bonds and constraints (using the gmxdump and .tpr specified in the command line).

Once the parsing is done, check the representations (Graphics > Representations menu): you need one representation containing the beads involved in the bonds/constraints; to see the backbone for instance, you need to create a new representation (Create Rep) in the good molecule (you have to select it in the top menu), and change it to name "B.*" (editable field named Selected Atoms).

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Kargar
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12 years 10 months ago #714 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

Dear xavier

I searched different kinds of scripts to visual my CG system with VMD. I found 2 of them but with limitations. I was very happy when I saw cg_bonds.tcl script on your site. Before any post I tried different kinds of ways included what you mentioned. after that I started posting. I know it is up to me to solve my problem but now I am confused and do not know what to do. I want a help or something like a starter to help me continue. It was the reason I wrote "I am looking forward hearing from you" to Clement.

Regard

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Clement
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12 years 10 months ago #715 by Clement

Replied by Clement on topic cg_bonds.tcl script

Did it work? Is it working now? Please let me know... It will help me to write a small tutorial about it.

Sorry to ask that, but what are the other things you find? It certainly had some functionality I could add to the current script (if respective authors allow it of course).

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Kargar
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12 years 10 months ago #716 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

I am so sorry to say "no, it does not work for me".

The 2 scripts I found are in GROMACS site :" www.gromacs.org/Developer_Zone/Programmi...de/VMD?highlight=vmd "
The top2psf.pl is specially for MARTINI ff. It works well for systems containing one part e.g protein or lipid. I tried it in a system of 1 protein and water. it worked. But top2psf.pl did not worked in my new system "what you know it" with 8 proteins. I asked Justin Lemkul, who wrote the script, about my problem and I found that I must change my topology file which it is difficult for "my system".
I also tried coarse_grain.tcl but I faced errors that I could not solve it so I abandoned it.

Thank you very much
Kargar

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Kargar
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12 years 10 months ago #717 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

Clement wrote: Did it work? Is it working now? Please let me know... It will help me to write a small tutorial about it.

Sorry to ask that, but what are the other things you find? It certainly had some functionality I could add to the current script (if respective authors allow it of course).

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Clement
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12 years 10 months ago #718 by Clement

Replied by Clement on topic cg_bonds.tcl script

Ok. Here is what we will do:

I will send you a 8-I-100ns-water.vmd file.

Copy the four files (cg_bonds.tcl, 8-I-100ns-water.gro, 8-I-100ns-water.tpr and 8-I-100ns-water.vmd) in the same directory. Go to that directory (in a command line window). Then:

$ vmd -e 8-I-100ns-water.vmd

The line above will load the 8-I-100ns-water.vmd file, which will read the 8-I-100ns-water.gro and 8-I-100ns-water.tpr files you sent me, using the /usr/local/bin/gmxdump executable, and create the representation I used to render the snapshot I sent you.

In a nutshell:

$ mkdir tmp_bonds
$ cp /path/to/my/files/8-I-100ns-water.{gro,tpr,vmd} tmp_bonds
$ cp /path/to/the/script/cg_bonds.tcl tmp_bonds
$ cd tmp_bonds
$ vmd -e 8-I-100ns-water.vmd

If you want to understand what I did, check the last lines of the 8-I-100ns-water.vmd file (you can retype these lines whenever you want in the command line window of VMD to redo everything). You can also load the 8-I-100ns-water.vmd file using the File > Load Visualization State menu of VMD (at least it's called like that in VMD 1.9), if you run it in the good directory.

If it doesn't work (please let me know), I think you need to check the versions of gromacs, VMD, ... you're using. I will explain a little bit more how the script works on the website, then you'll probably see what you're doing wrong.

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Kargar
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12 years 10 months ago #719 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

Hi Clement

Thank you very much for your good and useful explanations. There is no bond. The version of my GROMACS is 4-0-7 and my VMD is 1.8.5. I am going to install the new version of VMD. How about GROMACS? Should I install the new version? If yes I think, maybe I will face some problems and I have to start my simulations again :O

Thank you very much
Kargar

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Clement
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12 years 10 months ago #720 by Clement

Replied by Clement on topic cg_bonds.tcl script

Answers to your questions:

I tried with both VMD 1.8.7 and VMD 1.9. Maybe switching to the last version will fix the thing (I hope so!).
You don't need to compile any other version of gromacs since the informations you need (bonds and constraints) are present in your .tpr file (I was able to draw them).

New questions: what VMD tells you when you load the .vmd file? No errors? Does it show the table listing bonds and constraints?

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Kargar
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12 years 10 months ago #721 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

Clement wrote: Answers to your questions:

I tried with both VMD 1.8.7 and VMD 1.9. Maybe switching to the last version will fix the thing (I hope so!).

You don't need to compile any other version of gromacs since the informations you need (bonds and constraints) are present in your .tpr file (I was able to draw them).

New questions: what VMD tells you when you load the .vmd file? No errors?

Answer: There are no errors and every thing seems well.

Clement wrote: Does it show the table listing bonds and constraints?

Answer: Yes, it does. like before without any errors and warnings.

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Clement
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12 years 10 months ago #722 by Clement

Replied by Clement on topic cg_bonds.tcl script

Then I think maybe the version of VMD is the problem. Could you please test that for us? Installing the last version of VMD (1.9), go to the same directory as before and load the .vmd file (vmd -e 8-I-100ns-water.vmd)?

It works perfectly on our machines, with your files. Guess it's the last thing on your side which could cause a problem...

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Kargar
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12 years 10 months ago #723 by Kargar

Replied by Kargar on topic cg_bonds.tcl script

Hi Clement

****THANK YOU VERY MUCH****

It works with VMD-1.9. I did it with your .vmd file and also the steps I did before (source cg_bonds.tcl , ...); it works well:=D .Thank you for your help.

Best wishes
Kargar

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Clement
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12 years 10 months ago #724 by Clement

Replied by Clement on topic cg_bonds.tcl script

Thanks to you too! We now know that the cg_bonds.tcl script does not work with VMD 1.8.5 or anterior. We should have checked that before!

I updated the page ( http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/163-rb ) to take that into account.

Groetjes,
Clement

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