[gmx-users] Re: Genion and number of Ions (David van der Spoel)

David spoel at xray.bmc.uu.se
Wed Sep 25 20:57:22 CEST 2002

On Wed, 2002-09-25 at 19:23, Marc Saric wrote:
> David van der Spoel wrote:
> >> 2. Question: What to do with fractional charges (i.e. -3.2 ?)
> > 
> > That is wrong. There must be an error in your topology.
> I checked the input-pdb-file:
> It consists of 3 protein-strands without modifications etc., one MG-ion 
> and some waters (ligand has been removed before for separate processing).
It is quite easy to find the problem. Look at the .top file, in the
rightmost column in the atoms section you will see qtot (total charge
starting from atom 1). After each residue this number should be integer
(although small round off errors may occur).

The problem is most likely a N- or C-terminus for which you selected
none iso NH3+ or something like that.

> To check for the error, I have split the file into two parts:
> Protein
> Water+ion
> grompp reports a charge of +2 for Water+Ion as expected (Mg) but 
> something weird for the protein (-2.39e+1).
> I double-checked, that all atoms are there and that the termini are 
> correctly "capped" with OXT-atoms, but still, conversion gives the 
> charge-warning.
> Any explanation (beside "must be a broken pdb-file")?
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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