- Posts: 8
Visualizing a CG lipid in VMD
- zidarko
-
Topic Author
- Offline
- Fresh Boarder
Less
More
8 years 5 months ago #5267
by zidarko
Visualizing a CG lipid in VMD was created by zidarko
Hi,
I have recently did the protein aggregation tutorial nad I'm now trying to visualize the trajectories in VMD (1.9.2).
First I load the PDB file with only the protein part, followed by the trajectory in XTC format.
The I source the cg_bonds.tcl and I issue this command to draw the bonds:
vmd > cg_bonds -top protein.top -topoltype "martini"
But VMD fails:
atomsel : setbonds: Need one bondlist for each selected atom
Any idea what to try?
I tried to load the TPR file but I can't do it because the simulation files (TPR, TRR, XTC, ...) were produced by Gromacs 5.1.1 that doesn't have the gmxdump utility anymore (replaced by "gmx dump"). I also changed the operating system (OS X -> Linux) but the problem persists.
Thanks,
Jernej
I have recently did the protein aggregation tutorial nad I'm now trying to visualize the trajectories in VMD (1.9.2).
First I load the PDB file with only the protein part, followed by the trajectory in XTC format.
The I source the cg_bonds.tcl and I issue this command to draw the bonds:
vmd > cg_bonds -top protein.top -topoltype "martini"
But VMD fails:
atomsel : setbonds: Need one bondlist for each selected atom
Any idea what to try?
I tried to load the TPR file but I can't do it because the simulation files (TPR, TRR, XTC, ...) were produced by Gromacs 5.1.1 that doesn't have the gmxdump utility anymore (replaced by "gmx dump"). I also changed the operating system (OS X -> Linux) but the problem persists.
Thanks,
Jernej
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
8 years 4 months ago #5285
by Clement
Replied by Clement on topic Visualizing a CG lipid in VMD
Your system contains more than just the protein. Is your .top describing the number of water also? As the error messages says, you need to make sure the .top describes every single molecule in there.
Cheers,
Cl.
Cheers,
Cl.
Please Log in or Create an account to join the conversation.
- earosenz
-
- Visitor
8 years 2 months ago #5388
by earosenz
Replied by earosenz on topic Visualizing a CG lipid in VMD
I'm having the same issue, but there isn't anything other than protein in my system.
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
8 years 2 months ago #5391
by Clement
Replied by Clement on topic Visualizing a CG lipid in VMD
More details?
Please Log in or Create an account to join the conversation.
- mrz2010
-
- Offline
- Fresh Boarder
Less
More
- Posts: 4
8 years 1 month ago #5398
by mrz2010
Replied by mrz2010 on topic Visualizing a CG lipid in VMD
I am having the exact same error when I try to add bonds to my file. I have a simple DPPC bilayer with the water removed, but when I use the command cg_bonds -top DPPC.top -topoltype "elastic" it gives the same error as described in the first post. Has anyone found a solution to or cause of this problem?
I thought it was a problem with my topology file, so I tried a couple options with no success:
1. topology with just the #include statements to the force field files, and then the [system] and [molecules] sections
2. topology with the DPPC information lifted from the martini lipids itp file, no #include statements, and then the [system] and [molecules] sections
My topology file describes everything included in the .gro file that I upload to VMD. In fact, I used the cg_bonds.tcl script a couple years ago successfully, but I cannot figure out why I am getting this error now. Any help would be appreciated.
I thought it was a problem with my topology file, so I tried a couple options with no success:
1. topology with just the #include statements to the force field files, and then the [system] and [molecules] sections
2. topology with the DPPC information lifted from the martini lipids itp file, no #include statements, and then the [system] and [molecules] sections
My topology file describes everything included in the .gro file that I upload to VMD. In fact, I used the cg_bonds.tcl script a couple years ago successfully, but I cannot figure out why I am getting this error now. Any help would be appreciated.
Please Log in or Create an account to join the conversation.
- peterkroon
-
- Offline
- Gold Boarder
Less
More
- Posts: 210
8 years 1 month ago #5409
by peterkroon
Replied by peterkroon on topic Visualizing a CG lipid in VMD
You can try to use the -tpr option. If you're using Gromacs 5.x, you have two options:
1)(untested)
2) change the cg_bonds.tcl script. Change line 491 fromtoand run
1)
cg_bonds -tpr my_simulation.tpr -gmx "/path/to/gromacs5/bin/gmx dump"2) change the cg_bonds.tcl script. Change line 491 from
set gmxdump "/path/to/gromacs4/bin/gmxdump"set gmxdump "/path/to/gromacs5/bin/gmx dump"cg_bonds -tpr my_simulation.tprPlease Log in or Create an account to join the conversation.
- mrz2010
-
- Offline
- Fresh Boarder
Less
More
- Posts: 4
8 years 1 month ago #5411
by mrz2010
Replied by mrz2010 on topic Visualizing a CG lipid in VMD
Thanks for the advice, but I am using Gromacs v. 4.6.7; also, I am trying to visualize the system using a computer which does not have Gromacs installed. From my understanding, the -tpr option only works when you provide a path to the gromacs installation.
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
8 years 1 month ago #5412
by Clement
Replied by Clement on topic Visualizing a CG lipid in VMD
Sorry, missed your answer. Why are you providing this -topoltype "elastic" flag? Do you have an elastic network in your system?
Please Log in or Create an account to join the conversation.
- mrz2010
-
- Offline
- Fresh Boarder
Less
More
- Posts: 4
8 years 1 month ago #5413
by mrz2010
Replied by mrz2010 on topic Visualizing a CG lipid in VMD
My system is a simple DPPC bilayer. I have been using the -topoltype "elastic" flag because that is what is suggested on the tutorials on the MARTINI website. Regardless, I have also tried -topoltype "martini" and receive the same error.
Since the cg_bonds tool has worked for me before, I think there must be a problem with one of my input files, likely the topology file. However, after looking over my topology file multiple times, I am not sure where.
My current topology file looks like:
Where in this case I have lifted the molecule type directly from the "martini_v2.0_lipids.itp" file. I have also tried to include this file such the the topology file looks like:
With either version I still arrive at the originally described error.
Since the cg_bonds tool has worked for me before, I think there must be a problem with one of my input files, likely the topology file. However, after looking over my topology file multiple times, I am not sure where.
My current topology file looks like:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
#include "martini_v2.2.itp"
[moleculetype]
; molname nrexcl
DPPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DPPC NC3 1 1.0
2 Qa 1 DPPC PO4 2 -1.0
3 Na 1 DPPC GL1 3 0
4 Na 1 DPPC GL2 4 0
5 C1 1 DPPC C1A 5 0
6 C1 1 DPPC C2A 6 0
7 C1 1 DPPC C3A 7 0
8 C1 1 DPPC C4A 8 0
9 C1 1 DPPC C1B 9 0
10 C1 1 DPPC C2B 10 0
11 C1 1 DPPC C3B 11 0
12 C1 1 DPPC C4B 12 0
[bonds]
; i j funct length force.c.
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.370 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
6 7 1 0.470 1250
7 8 1 0.470 1250
4 9 1 0.470 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
4 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
[ system ]
DPPC BILAYER
[ molecules ]
DPPC 15120
[moleculetype]
; molname nrexcl
DPPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DPPC NC3 1 1.0
2 Qa 1 DPPC PO4 2 -1.0
3 Na 1 DPPC GL1 3 0
4 Na 1 DPPC GL2 4 0
5 C1 1 DPPC C1A 5 0
6 C1 1 DPPC C2A 6 0
7 C1 1 DPPC C3A 7 0
8 C1 1 DPPC C4A 8 0
9 C1 1 DPPC C1B 9 0
10 C1 1 DPPC C2B 10 0
11 C1 1 DPPC C3B 11 0
12 C1 1 DPPC C4B 12 0
[bonds]
; i j funct length force.c.
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.370 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
6 7 1 0.470 1250
7 8 1 0.470 1250
4 9 1 0.470 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
4 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
[ system ]
DPPC BILAYER
[ molecules ]
DPPC 15120
Where in this case I have lifted the molecule type directly from the "martini_v2.0_lipids.itp" file. I have also tried to include this file such the the topology file looks like:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
#include "martini_v2.2.itp"
#include "martini_v2.0_lipids.itp"
[ molecules ]
DPPC 15120
#include "martini_v2.0_lipids.itp"
[ molecules ]
DPPC 15120
With either version I still arrive at the originally described error.
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
8 years 1 month ago - 8 years 1 month ago #5414
by Clement
Replied by Clement on topic Visualizing a CG lipid in VMD
Mmmmh... Sorry to insist, but do you have exactly 15120*12=181440 beads in your system?
And... you don't need to provide any -topoltype here. Only lipids is the default topology type, which is "martini".
And... you don't need to provide any -topoltype here. Only lipids is the default topology type, which is "martini".
Last edit: 8 years 1 month ago by Clement.
Please Log in or Create an account to join the conversation.
- mrz2010
-
- Offline
- Fresh Boarder
Less
More
- Posts: 4
8 years 1 month ago #5415
by mrz2010
Replied by mrz2010 on topic Visualizing a CG lipid in VMD
Yes, my system has the correct number of beads, and I get the same error without providing any -topoltype.
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
8 years 1 month ago #5416
by Clement
Replied by Clement on topic Visualizing a CG lipid in VMD
Could you send me your conformation/topologies?
Please Log in or Create an account to join the conversation.
- zidarko
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
8 years 1 month ago #5417
by zidarko
Replied by zidarko on topic Visualizing a CG lipid in VMD
What helped me some time ago was to recreate the job run file (.TPR) in Gromacs 5.0.7 (i.e. Gromacs < 5.1). Afterwards I was able to load the coarse grained trajectory in VMD.
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
8 years 1 month ago #5418
by Clement
Replied by Clement on topic Visualizing a CG lipid in VMD
EDIT: problem solved. It seems that in some cases, the format of the .itp file is problematic for the cg_bonds.tcl script. Too much tabulation ("\t") or something. Replacing them with spaces should do the trick (vi does that very well).
Please Log in or Create an account to join the conversation.
- mostafamjm
-
- Offline
- Fresh Boarder
Less
More
- Posts: 1
7 years 6 months ago #5946
by mostafamjm
Replied by mostafamjm on topic Visualizing a CG lipid in VMD
Hi,
Problem solved; Just make a new line at the end of your Topology.top file (e.g. if the last line of [molecules] directive in your .top file is (NA+ 100) put the cursor at the end of this line and make a new line simply by hiting enter key.) and save your .top file.
Cheers
Problem solved; Just make a new line at the end of your Topology.top file (e.g. if the last line of [molecules] directive in your .top file is (NA+ 100) put the cursor at the end of this line and make a new line simply by hiting enter key.) and save your .top file.
Cheers
Please Log in or Create an account to join the conversation.
- dengjinxia
-
- Visitor
7 years 3 weeks ago #7206
by dengjinxia
Replied by dengjinxia on topic Visualizing a CG lipid in VMD
I am a new user to gromacs, and find online script to render bond for groma cs file by VMD.
The script is cg_bonds.tcl.
After source the above script in TK console, and run it, I got an error as:
"File: /toppar/martini_v2.2.itp not exists."
I check the script and try to modify the path so that it can find the right= parameter file which all in my current working directory, but can find no = where specify the above path.
So, wonder how to fix this problem, and looking forward your advice on this.
Best regards,
Nancy
The script is cg_bonds.tcl.
After source the above script in TK console, and run it, I got an error as:
"File: /toppar/martini_v2.2.itp not exists."
I check the script and try to modify the path so that it can find the right= parameter file which all in my current working directory, but can find no = where specify the above path.
So, wonder how to fix this problem, and looking forward your advice on this.
Best regards,
Nancy
Please Log in or Create an account to join the conversation.
- bart
-
- Offline
- Admin
Less
More
- Posts: 98
7 years 3 weeks ago #7207
by bart
Replied by bart on topic Visualizing a CG lipid in VMD
Hey Nancy,
What I usually do is to open vmd in the folder which contains all the tip files. I never found a way to point to their location in a correct way.
Cheers
What I usually do is to open vmd in the folder which contains all the tip files. I never found a way to point to their location in a correct way.
Cheers
Please Log in or Create an account to join the conversation.
- dengjinxia
-
- Visitor
7 years 3 weeks ago #7211
by dengjinxia
Replied by dengjinxia on topic Visualizing a CG lipid in VMD
Thank you Bart,
That's very helpful. I finally include the path in the .itp file and get the bond rendered.
It good for snapshot only, as MD goes on, the bond cross the cell, wonder any tool to fix that...
sorry, very new in gromacs :-)
thanks again,
Nancy
That's very helpful. I finally include the path in the .itp file and get the bond rendered.
It good for snapshot only, as MD goes on, the bond cross the cell, wonder any tool to fix that...
sorry, very new in gromacs :-)
thanks again,
Nancy
Please Log in or Create an account to join the conversation.
- peterkroon
-
- Offline
- Gold Boarder
Less
More
- Posts: 210
7 years 3 weeks ago - 7 years 3 weeks ago #7214
by peterkroon
Replied by peterkroon on topic Visualizing a CG lipid in VMD
Double post, please delet
Last edit: 7 years 3 weeks ago by peterkroon.
Please Log in or Create an account to join the conversation.
- peterkroon
-
- Offline
- Gold Boarder
Less
More
- Posts: 210
7 years 3 weeks ago #7215
by peterkroon
Replied by peterkroon on topic Visualizing a CG lipid in VMD
You can try converting your trajectory to tng format, and load that in vmd, or use gmx trjconv to fix the PBC.
Please Log in or Create an account to join the conversation.
Time to create page: 0.201 seconds