AMBER Archive (2008)

Subject: RE: AMBER: Problems with the charge (membrane simulation)

From: Ross Walker (
Date: Thu Aug 07 2008 - 10:18:12 CDT

Hi Rebeca,

> I am trying to do a membrane+protein simulation using 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 use this force field in NAMD, I can see that the total charge is
> not
> zero, as is logical.
> Info: TOTAL CHARGE = -0.94832 e
> So, some warnings appear:
> 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,

You should probably try and find out where the missing charge is. 0.052 is
too much to just be rounding errors. This suggests to me that you have an
atom missing, probably a hydrogen, or one too many atoms somewhere. Check
that each of you pieces is neutral. I.e. is the protein neutral? Then what
about each of the lipid molecules? What parameters are you using for the

You could simply tell leap to add 23 sodium atoms instead and just ignore
the 0.052 but in this case it is probably telling you about a deeper

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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