Problems with the charge (membrane simulation)

From: rebeca_at_mmb.pcb.ub.es
Date: Wed Aug 06 2008 - 13:18:34 CDT

Hello,
I am trying to do a membrane+protein simulation using NAMD and the Amber force
field. I have ionized with tleap, and the charge of my system was -22.95, so
Leap added 22 Na+ ions to neutralize:

 addions solvated Na+ 0
22 Na+ ions required to neutralize.

When I tried to minimize with NAMD I can see that the total charge is almost 1:

Info: TOTAL CHARGE = -0.94832 e

So, some warnings appear:

Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global bond count!
Warning: Bad global angle count!
Warning: Bad global dihedral count!

Shoud I add 23 Na+ instead of the default Leap applies? In such way, the charge
won´t be exactly zero, either. Do you think will be there problems, too?

Thank you very much for your help,

Best wishes,

Rebeca García Fandiño
Parc Cientific of Barcelona
rebeca_at_mmb.pcb.ub.es

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