search

akohlmey / topotools

VMD plugin for manipulating topology information
Other
28 stars 16 forks source link

Incorrect dihedral type when the structure contains three-membered ring #17

Closed xu139411 closed 4 years ago

xu139411 commented 4 years ago

When the structure has a three-membered ring (e.g., an epoxide group), TopoTools will create an incorrect type of dihedral in which the first and last atom are the same.

How to reproduce this error: 1) Open VMD 1.9.3 and then the TK console. Load the data: topo readlammpsdata pGO.data full

The data file is a graphene oxide with epoxides and hydroxyls on its surface. The atom type and bond type is based on (https://doi.org/10.1016/j.commatsci.2015.12.030).

2) Generate angles and dihedrals topo guessangles topo guessdihedrals

3) Export the data: topo writelammpsdata pGO_with_angle_dihedral.data full

In the generated data file, dihedral type 24 is the incorrect dihedral type. An example is dihedral 63: 63 24 162 7 8 162.

TopoTools has helped my research a lot. Thanks for providing such a tool!

datafile.zip

akohlmey commented 4 years ago

Thanks for reporting. This should be fixed with commit 0bc3951f707420a2651b403ce8eddc6c7dfbaa57 Please download a copy of the latest plugin from https://github.com/akohlmey/topotools/archive/master.zip, create a folder topotools1.8 next to the existing topotools1.7 folder of your VMD installation and copy all the .tcl files there. You can test, if this worked in the VMD console:

vmd > package require topotools
1.8
vmd >

If it shows 1.7, the installation of the update package failed.

xu139411 commented 4 years ago

This is to confirm that commit 0bc3951 fixes the problem after testing on the original graphene oxide structure as well as a larger one.

Thanks!

akohlmey commented 4 years ago

issue is resolved with the latest changes. They will be included in VMD after a few more other changes are completed.