Hello,
I am just learning to use gromacs following this tutorial:
http://www.mdtutorials.com/gmx/complex/02_topology.html
In the tutorial there is a script for rearranging the bond order of the JZ4 file so that it can be used in gromacs, however it requires a version of python that the terminal I'm using doesn't have, and I don't have the ability to change that. How would I go about manually reordering the bonds?
Justin Lemkul
My bond reordering script is written in Perl and should be executable by any interpreter.
The Python dependency is something that I can't change, sorry. That's required to convert the CGenFF .str file to GROMACS .itp format.
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