VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Tue Nov 18 2008 - 19:40:24 CST

Hi all,
 
1- I was wondering what is the importanced of the ionic concentration in the mentioned script at this webpage: http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/
 
autoionize -psf file.psf -pdb file.pdb -is 0.05
 
Is it to resemble the physiological pH? What if I didn't include it in the script, is there a default value for it?
 
2- Which would be more accurate: calculating the net charge on the peptide and specifying the number of opposiite charge to neutralize it - provided it is reasonably small, or using the autoionize
 
Thanks
Rabab