VMD-L Mailing List

From: Stojanoski, Vlatko (stojanos_at_bcm.edu)
Date: Fri Oct 23 2015 - 12:10:58 CDT

Dear vmd users,

How do I go about and create parameters for iodide and bromide ions?

I tried to find out on my own but no luck. Before it was suggested to me that I should look at the http://mackerell.umaryland.edu/charmm_ff.shtml or use VEGA ZZ (I didn't explore this option because our lab has only mac and VEGA ZZ is unavailable for mac, unfortunately) and go though the manual and tutorial files (this I did extensively and I learned a lot). However, I can not located any parameter files for iodide and bromide (maybe I'm not looking at the right place).

Since these are initial ions, I tried generating psf files using psfgen in order to proceed and use ffTK to generate the missing parameters but psfgen fails with error message(iodide in this case):

psfgen) Info: generating structure...psfgen) unknown residue type IOD failed!

I'm not sure what the residue type for iodide is?

I also, try to look this up but no luck.

Any suggestions or reference pointing to the right direction will be greatly appreciated. Thank you beforehand!

Vlatko