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Visualizing a CG lipid in VMD
- zidarko
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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
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- Clement
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Cheers,
Cl.
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- earosenz
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- Clement
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- mrz2010
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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.
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- peterkroon
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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.tpr
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- mrz2010
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- Clement
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- mrz2010
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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:
[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:
#include "martini_v2.0_lipids.itp"
[ molecules ]
DPPC 15120
With either version I still arrive at the originally described error.
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- Clement
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And... you don't need to provide any -topoltype here. Only lipids is the default topology type, which is "martini".
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- mrz2010
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- Clement
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- zidarko
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- Clement
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- mostafamjm
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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
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- dengjinxia
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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
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- bart
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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
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- dengjinxia
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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
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- peterkroon
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- peterkroon
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