[PyMOL] APBS plugin for Sugars

[Mario G. U. <ma...@cm...>]

Hi all,

I was trying to generate dipole moments with pymol using the APBS plugin. For proteins I adapted a code and the dipole moments are correct and work just fine, but for sugars it does not. I am well aware that the problem is that many of the residues are not present in the AMBER force field data (or the force field I want to use.) In APBS it is relatively easy to adapt and introduce the sugars' information manually, however in the APBS plugin for pymol gets a little bit thorny. I cannot seem to find the files where I should store the sugar information. Has anybody done this before? Any alternatives with other programs or approaches are also welcome.

Thank you in advance,

Mario