VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Oct 26 2015 - 19:29:41 CDT
The CHARMM General Forcefield (CGenFF) provides coverage for aryl iodide and aryl bromide, as well as some alkyl bromides. I suggest looking through the CGenFF topology file to see if you can find something workable.
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 thehttp://mackerell.umaryland.edu/charmm_ff.shtml
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!