VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Jun 20 2018 - 17:06:36 CDT

Dear Bargeen,

You are not missing anything, QwikMD currently selects the entire residue
when preparing QM regions including protein and nucleic residues to make
sure that no charge groups is broken creating QM regions with fractional
charges, and to keep the total charge of the system constant.

You can find more information at http://www.ks.uiuc.edu/Research/qmmm/#LACCG.
One can always edit the *_qm-input.pdb that defines the qm region (beta
column) and the QM-MM bonds (occupancy column) to meet their needs. Make
sure that you updated the total charge in *.conf file as well, if needed or
course.

We are evaluating ways of changing this behavior without introducing
errors.

Best

João 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851