Closed benjha closed 5 years ago
This is tested on XSEDE Bridges (vmd 1.9.2), so I would say tcl files are working. I will try to replicate malloc
issue on my side.
FYI, voltool
was introduced from 1.9.4 alpha (July 2019) according to here: https://www.ks.uiuc.edu/Research/vmd/vmd-new/devel.html
Simple MDFF using EnTK.ipynb
is based on 2009 Simple MDFF example:
Thus older VMD is needed.
@benjha @lee212 yes, voltool is a new feature added to VMD 1.9.4 (alpha) as I mentioned during our call. The 1.9.4 version as of today from the VMD download website (UIUC) remains a test version. Until, full release I recommend using 1.9.3. XSEDE resource Bridges has 1.9.2 installed as a module.
@lee212 @daipayans
Inspecting the
Simple MDFF using EnTK.ipynb
file, I notedthird_stage.tcl
does not correspond to "Rigid-body docking the structure into the density map" from:https://www.ks.uiuc.edu/Training/Tutorials/science/mdff/tutorial_mdff-html/
Are you following the 2019 "A simple MDFF example" ?
Anyway, when following the example on SUMMIT and Mac (Mac binaries downloaded from VMD site) the "Rigid-body docking the structure into the density map" code:
gives the next error on Mac:
and in SUMMIT:
Could you verify "A simple MDFF example" in your local systems? I'd like to confirm there is a bug with VMD and report the bug.
These are the commands from stage one to three:
Thanks!,
Benjamin