VMD-L Mailing List

From: Shaherin Basith (shaherinb_at_gmail.com)
Date: Fri Jan 11 2013 - 02:06:22 CST

Dear VMD support team,

I'm trying to neutralize the protein-DNA complex system using 'Autoionize'
plugin in VMD.

The plugin calculates:

System net charge before adding ions: -20.81999099254608e.
Ions to be placed: 20 SOD
System net charge after adding ions: -0.8199909925460815e.

Then an error message reads as follows:
"System has a non-integer total charge. There was likely a problem in the
process of building it."

The.pdb and .psf files were created using VMD 1.9.1.

Due to this error, when I subjected the ionized system for NAMD simulation
it showed strange energy levels and the program eventually stopped as
"Exiting prematurely."
In this situation, I'm not sure if the net charge of system caused the
failure of equilibration with NAMD.

Please help me in this regard.

Thanking you in anticipation.

Regards, 

-- 
Shaherin Basith
Phd Student
Systems Biology lab
Ajou University
Suwon
South Korea
e-mail: shaherinb_at_ajou.ac.kr
Mobile: 010-6873-1033