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Issues with cg_bonds.tcl and polarizable Martini in VMD
- johnd
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7 years 2 months ago #7092
by johnd
Issues with cg_bonds.tcl and polarizable Martini in VMD was created by johnd
Hi,
I have started working with the polarizable martini forcefield (v2.2P), however VMD seems to be unable to draw in the bonds when using cg_bonds.tcl.
The command and error:
vmd > cg_bonds -top topol_a.top
atomsel : setbonds: Need one bondlist for each selected atom
This also happens if "-topoltype martini" is added
Just to cover my bases:
Protein in vacuo
Beads represented in itp: 276
Beads in gro/pdb: 276
I have checked over the forum and found a few possible solutions
-Convert tabs in itp file to spaces ( cgmartini.nl/index.php/component/kunena/...-a-cg-protein-in-vmd )
> itp file had no tabs to start off with so that wasn't the issue
-add an empty line at the end of all top and itp files being called ( cgmartini.nl/index.php/rb )
> did this and still no luck
-Use cg_bonds with gmx dump to extract info from tpr ( cgmartini.nl/index.php/component/kunena/...zation-with-cg-bonds )
> also no luck
Any thoughts? I haven't run into such a stubborn issue with the regular forcefield before.
Cheers,
John
I have started working with the polarizable martini forcefield (v2.2P), however VMD seems to be unable to draw in the bonds when using cg_bonds.tcl.
The command and error:
vmd > cg_bonds -top topol_a.top
atomsel : setbonds: Need one bondlist for each selected atom
This also happens if "-topoltype martini" is added
Just to cover my bases:
Protein in vacuo
Beads represented in itp: 276
Beads in gro/pdb: 276
I have checked over the forum and found a few possible solutions
-Convert tabs in itp file to spaces ( cgmartini.nl/index.php/component/kunena/...-a-cg-protein-in-vmd )
> itp file had no tabs to start off with so that wasn't the issue
-add an empty line at the end of all top and itp files being called ( cgmartini.nl/index.php/rb )
> did this and still no luck
-Use cg_bonds with gmx dump to extract info from tpr ( cgmartini.nl/index.php/component/kunena/...zation-with-cg-bonds )
> also no luck
Any thoughts? I haven't run into such a stubborn issue with the regular forcefield before.
Cheers,
John
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- peterkroon
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7 years 2 months ago #7095
by peterkroon
Replied by peterkroon on topic Issues with cg_bonds.tcl and polarizable Martini in VMD
I always prefer using the -tpr option, since it generally produces less problems. What errors did you get there?
Alternatively (may be a bit of work), convert your trajectory to tng format (trjconv -f -s -o), and read that with vmd.
Alternatively (may be a bit of work), convert your trajectory to tng format (trjconv -f -s -o), and read that with vmd.
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- johnd
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7 years 2 months ago #7101
by johnd
Replied by johnd on topic Issues with cg_bonds.tcl and polarizable Martini in VMD
Hi Peter,
Thank you for your help,
Just using -tpr didn't work, nor -gmx /path/to/gmx -tpr
Error: Child process exited abnormally
I modified the tcl script to account for the fact I was using a 5.0.X series gromacs and then just using -tpr worked fine and vmd could render all the bonds properly
In case anyone is interested
Line 202: change $gmxdump to gmx dump
Line 491: /path/to/bin/GMXRC
Thank you for your help,
Just using -tpr didn't work, nor -gmx /path/to/gmx -tpr
Error: Child process exited abnormally
I modified the tcl script to account for the fact I was using a 5.0.X series gromacs and then just using -tpr worked fine and vmd could render all the bonds properly
In case anyone is interested
Line 202: change $gmxdump to gmx dump
Line 491: /path/to/bin/GMXRC
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- xavier
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7 years 2 months ago #7102
by xavier
Replied by xavier on topic Issues with cg_bonds.tcl and polarizable Martini in VMD
cg_bonds does not read tpr from 5.X up ... keep to the gmx4.6.X.
It has also not been made to read Martini22p ... but it might be able to ...
Most important make and use a downgraded tpr :)).
It has also not been made to read Martini22p ... but it might be able to ...
Most important make and use a downgraded tpr :)).
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7 years 2 months ago #7103
by xavier
Replied by xavier on topic Issues with cg_bonds.tcl and polarizable Martini in VMD
cg_bonds does not read tpr from 5.X up ... keep to the gmx4.6.X.
It has also not been made to read Martini22p ... but it might be able to ...
Most important make and use a downgraded tpr :)).
It has also not been made to read Martini22p ... but it might be able to ...
Most important make and use a downgraded tpr :)).
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- peterkroon
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7 years 2 months ago #7105
by peterkroon
Replied by peterkroon on topic Issues with cg_bonds.tcl and polarizable Martini in VMD
I've used it with gmx 5.1.4 without too much trouble - I did indeed modify the script to point to the right exectuble:
line 491:
set gmxdump "/my/path/to/gromacs 5.1.4/bin/gmx dump"
I didn't change line 202.
line 491:
set gmxdump "/my/path/to/gromacs 5.1.4/bin/gmx dump"
I didn't change line 202.
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- johnd
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7 years 2 months ago #7107
by johnd
Replied by johnd on topic Issues with cg_bonds.tcl and polarizable Martini in VMD
Xavier - Thank you for your input, I think the fact that it wasn't made for v2.2P is really the core reason for this error. However, I am inclined to agree with Peter, so long as the script is pointing to the correct executable it should be ok with other versions of gromacs, and saves the hassle of needing another version of gromacs on hand.
Changing line 202 probably wasn't necessary as 5.0.X and 5.1.X still have backwards compatibility with 4.X series command inputs, which is why it still worked with just line 491 modification, but I think this is slated to change with newer releases
Changing line 202 probably wasn't necessary as 5.0.X and 5.1.X still have backwards compatibility with 4.X series command inputs, which is why it still worked with just line 491 modification, but I think this is slated to change with newer releases
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- peterkroon
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7 years 2 months ago #7109
by peterkroon
Replied by peterkroon on topic Issues with cg_bonds.tcl and polarizable Martini in VMD
As long as the output of gmx dump doesn't qualitatively change it should be fine. I don't expect anything drastic in the (near) future. And in the far future, gromacs will probably move solely to tng trajectories, which contain the bonded information and make the script pointless.
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