volArea for coarse-grained trajectories

[sizeineb]

Dears,

I would like to compute the volume of an empty pocket (no ligand) over time from a coarse-grained trajectory (Martini Force field).

I was thinking to use volArea and choose a probe radius of a regular Martini bead. I would like to have your opinion about this, please. Is the tool adapted to coarse-grained trajectories?

Thank you in advance for your clarification.

Best,

Zeineb

[nscerqueira]

Dear Zeineb,

Volarea can be used to calculate the area or empty Volume of pockets of any chemical structure.
If you can load your simulation to VMD, these calculations are very straightforward. It only requires the selection of the atoms where these properties will be calculated. I would advice first to get the values of only a snapshot and only then go through the full simulations. The calculation of each frame requires some seconds depending on the cpu and memory available on the computers.

Hope this helps

Regards

Nuno

[sizeineb]

Dear Nuno,

Thank you very much for your fast reply.

I am trying to use VolArea on my Coarse-grained trajectory but I am getting the following error:

no such table: frame_0
no such table: frame_0
while executing
"$VolArea::namedb eval "SELECT sasa FROM frame_$i WHERE resname=:name""
(procedure "VolArea::calcall" line 10)
invoked from within
"VolArea::calcall"
(procedure "VolArea::RunButton" line 111)
invoked from within
"VolArea::RunButton"
invoked from within
".volarea.nb1.fp.rru.b1 invoke "
invoked from within
".volarea.nb1.fp.rru.b1 instate !disabled { .volarea.nb1.fp.rru.b1 invoke } "
invoked from within
".volarea.nb1.fp.rru.b1 instate pressed { .volarea.nb1.fp.rru.b1 state !pressed; .volarea.nb1.fp.rru.b1 instate !disabled { .volarea.nb1.fp.rru.b1 invo..."

I tried to change the dimensions of the analysis area, the scale, the cavity probe radius or calculate the volume on a small number of frames but I am still getting the same error and I can't really understand the error message. I would really appreciate your help on this, please.

Best,

Zeineb

[nscerqueira]

Hello, Please try running volarea with a single structure from your simulation. Load the pdb ( or other file format) and then run volarea. Remember that the Structure that is read in volarea is the top molecule of VMD. The error maybe is related with this issue. Regards Nuno Nuno M. F. S. A. Cerqueira www.fc.up.pt/pessoas/nscerque nscerque@fc.up.pt No dia 13/08/2019, às 09:54, sizeineb <notifications@github.com> escreveu: Dear Nuno, Thank you very much for your fast reply. I am trying to use VolArea on my Coarse-grained trajectory but I am getting the following error: no such table: frame_0 no such table: frame_0 while executing "$VolArea::namedb eval "SELECT sasa FROM frame_$i WHERE resname=:name"" (procedure "VolArea::calcall" line 10) invoked from within "VolArea::calcall" (procedure "VolArea::RunButton" line 111) invoked from within "VolArea::RunButton" invoked from within ".volarea.nb1.fp.rru.b1 invoke " invoked from within ".volarea.nb1.fp.rru.b1 instate !disabled { .volarea.nb1.fp.rru.b1 invoke } " invoked from within ".volarea.nb1.fp.rru.b1 instate pressed { .volarea.nb1.fp.rru.b1 state !pressed; .volarea.nb1.fp.rru.b1 instate !disabled { .volarea.nb1.fp.rru.b1 invo..." I tried to change the dimensions of the analysis area, the scale, the cavity probe radius or calculate the volume on a small number of frames but I am still getting the same error and I can't really understand the error message. I would really appreciate your help on this, please. Best, Zeineb — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[sizeineb]

Dear Nuno,

Thank you for your reply.

I tried to run volArea with a single structure from my simulation (coarse-grained) and another all-atoms structure from the PDB, using Linux and macOS machines, but I am still getting problems with the volume calculation.

In the VolArea window:

• When I check only the "Surface calculation" --> I have no problems, the calculation finish without any problems.

• When I check only the "Volume calculations" --> I am getting the previously mentioned error: "no such table: frame_0"

• When I check both "Surface calculation" and "Volume calculation" --> I am getting another error:
  missing operand at _@_ in expression "0 + _@_" missing operand at _@_ in expression "0 + _@_" (parsing expression "0 + ") invoked from within "expr $sum + $val" (procedure "VolArea::calcall" line 11) invoked from within "VolArea::calcall"

The structure that I want to analyze is the top molecule in VMD.

I am doing tests on the PDB structure 2MGY. I would really appreciate if you can try to compute the volume of the ligand pocket and see if the error is reproducible or maybe I am messing up with the parameters that I am using.

Thank you in advance for your help.

Best,

Zeineb