normal Error in using cg_bonds.tcl

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8 years 7 months ago - 8 years 7 months ago #3729 by Logan
Error in using cg_bonds.tcl was created by Logan
I have a question for using cg_bonds.tcl with VMD. Followings are the procedure I took from which I got error at the end. Could you please let me know why this is happened or any possibility of bugs in the cg_bonds.tcl?

1) Take xx.pdb file from Protein Data Bank
2) ./martinize.py -f xx.pdb -o system.top -x cg_xx.pdb -ff martini21 -ss xx.dssp -elastic (here xx.dssp is taken from www.cmbi.ru.nl/hsspsoap/ by using xx.pdb downloaded in the previous step)
3) In VMD, sourcing and cg_bonds -top system.top

This works for some proteins to show elastic network in VMD but mostly not working with the error "invalid atom id"

Could you please let me know what is the problem.

Thanks
Last edit: 8 years 7 months ago by Logan.

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8 years 7 months ago - 8 years 7 months ago #3738 by Clement
Replied by Clement on topic Error in using cg_bonds.tcl
You have to provide the flag -topoltype "elastic" to cg_bonds... That should improve its behavior for a start.

Then, this script seems to be... unstable with the topologies written with martinize.py. Comes from the order bond/constraints are read. I wrote another script to do exactly the same thing, but in a most robust way; it's going to be released at some point.

Note that if you want to use an elastic network on your protein, we recommend ElNeDyn... Flag -ff elnedyn in martinize.py I believe.
Last edit: 8 years 7 months ago by Clement.

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8 years 7 months ago #3749 by Logan
Replied by Logan on topic Error in using cg_bonds.tcl
Thank you for your comments!

I tried things you recommended but it did not work through.

cg_bonds -top system.top -topoltype "elastic" still generated error message of "invalid atom id" with both -ff elnedyn and -ff martini21 in using martinize.py

Could you recommend any other script for generating CG model of PDB protein?

Best,

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8 years 7 months ago #3750 by Clement
Replied by Clement on topic Error in using cg_bonds.tcl
Could you send me topologies (.itp, .top) and conformations (.gro) you're working with? I'm going to try to see where the problem is.

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8 years 7 months ago #3751 by Logan
Replied by Logan on topic Error in using cg_bonds.tcl
How can I send you those files? Could you give me your e-mail address?

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8 years 7 months ago #3752 by Clement
Replied by Clement on topic Error in using cg_bonds.tcl
I seem to remember you sent something (the same text as your first post down here) to me already... Use the same one.

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3 years 3 months ago #8236 by Xotic
Replied by Xotic on topic Error in using cg_bonds.tcl
I am facing the same issue "invalid atom id", this thread is 5 years old and there was no update regarding the solution to this thread. Does anyone have a fix?

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3 years 3 months ago #8237 by bart
Replied by bart on topic Error in using cg_bonds.tcl
For one you should use the newest cg_bonds:
cgmartini.nl/images/tools/VMD/cg_bonds-v5.tcl

Then with this I usually do the following which works for an extreme wide range of tested protein and dsDNA models using elastic networks.

1) load gro, xtc (or only gro)
2) type in the vmd command line:
cg_bonds -topoltype "elnedyn" -color "orange" -mat "AOChalky" -res 52 -rad 0.2 -top ./topol.top
3) if you have too many bonds to be drawn in VMD (a problem due to the AA focus of VMD), you can add -cutoff 7.5 (works almost all the time) for showing the bonds, though you are now not showing all bonds, which might or might not be considered cheating. You can get around this by asking for a special build on the VMD mailing list which has a higher maximum value of bonds per atom.

This assumes that the topology file is in the same folder as the currently active folder in VMD. You can just change directories using the VMD terminal until this is true, or open VMD in the folder containing the topol. It is important to prepend it with ./ otherwise you get a pointing error in VMD, which might or might not be clear at all (this should all be true for VMD version >= 1.9.3).

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3 months 2 weeks ago #9482 by aguljas
Replied by aguljas on topic Error in using cg_bonds.tcl
I've been having the same issue with "invalid atom id" using the newest cg_bonds-v5.tcl script. I'd like to analyze simulations that I've run using Martini 3, with a system generated using CHARMM-GUI. I've tried every possibility for -topoltype although none seem to work. Is the script not yet compatible with the newest version of Martini?

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3 months 12 hours ago #9494 by riccardo
Replied by riccardo on topic Error in using cg_bonds.tcl
Actually, I think cg_bonds is not necessary anymore in the latest versions of gromacs. One can use the following:

echo 0 | gmx trjconv -f run.gro -s run.tpr -conect -o run-conect.pdb -pbc whole
sed -i '/ENDMDL/d'  run-conect.pdb

And then:
vmd run-conect.pdb
or, for a trajectory:
vmd run-conect.pdb traj.xtc

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3 months 8 hours ago #9496 by bart
Replied by bart on topic Error in using cg_bonds.tcl
I wonder how many bonds can be drawn with the conect method. PDB is a fixed file format so there must be a limit. For small systems I completely agree that the conect method works very well.

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3 months 4 hours ago - 3 months 4 hours ago #9497 by buuhuu
Replied by buuhuu on topic Error in using cg_bonds.tcl
I think the limit is 12 per atom. VMD does not draw more than 12 bonds per atom. Thus, the above method works for anything but elastic network bonds.
Last edit: 3 months 4 hours ago by buuhuu.

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2 months 3 weeks ago #9500 by bart
Replied by bart on topic Error in using cg_bonds.tcl
That is a general issue. I meant the total amount of bonds that can be specified due ti the limited indexing. For example 9999 (I don't know by hard what the index limit is in the conect entry.)

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3 days 2 hours ago - 3 days 9 minutes ago #9546 by bqAlvii
Replied by bqAlvii on topic Error in using cg_bonds.tcl
Hi all. I dont know if this code may be used to visualize membrane only structures. Or exist any way to visualize membrane only structures, cause when i load my structure (.gro and .xtc) into VMD only gets dots (even if i change the representation to licorice, which has worked for me before).
echo 0 | gmx trjconv -f run.gro -s run.tpr -conect -o run-conect.pdb -pbc whole
sed -i '/ENDMDL/d'  run-conect.pdb

EDIT

I notice that the command was functionally perfect, just one extra space in sed editor generate the error.
Nothing wrong with the command. Thanks you all anyways.
Last edit: 3 days 9 minutes ago by bqAlvii.

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