[gmx-users] Hi all!

[David van der Spoel]

Marcelo Fabricio Masman wrote:
> Hi all!!!
> I am using the programme grompp (double precision) and the programme 
> genion to make  "neutral" .top and .tpr files. But after change the 
> quantity of H2O molecules and add the line with the necessary Na+ ions I 
> am still having WARNING and the charge is STILL  negative. What happend? 
> What am I doing wrong? Should I do something else?
> Here are the WARNING banners:
>  
> 
> Generated 243951 of the 243951 1-4 parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 2 bonded neighbours for SOL 41338
> WARNING 1 [file "Ab-1.top", line 5860]:
>   Too few parameters on line (source file toppush.c, line 1096)
> Excluding 2 bonded neighbours for 3 Na+
> WARNING 2 [file "Ab-1.top", line 5860]:
>   System has non-zero total charge: -3.000000e+00
> 
> processing coordinates...
> WARNING 3 [file "Ab-1.top", line 5860]:
>   Bad box in file Ab-1_n.gro

you have the wrong order of things in your topology file and you haven't 
updated the  number of atoms in the gro file (should be 6 fewer)

> Generated a cubic box   10.898 x   10.838 x   10.922
> double-checking input for internal consistency...
> renumbering atomtypes...
> 
> Thank you very much.
> 
> Marcelo
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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