[gmx-users] water overlaps gold bar

[Martin Höfling]

Hi all,

i have a gold crystal pdb which i wanna use in water. As far as i understood 
chapter 5, it's easier to bypass the pdb2gmx step.

genbox -cp ausf-editconf.pdb -o ausf-solvated.pdb -cs -p topolhandmade.top
My problem is that genbox is placing solvent inside the gold bar.

The pdb looks like:
...
ATOM    962  Au  AUS     1      66.099  23.309  44.866  1.00  0.00
ATOM    963  Au  AUS     1      66.099  23.309  52.043  1.00  0.00
...

My created include file goldsf.itp

[ bondedtypes ]
1 1 1 2
[ AUS ]
[ atoms ]
Au Au 0.000     0

[ atomtypes ]
Au   196.9665         0.14     A     0.4164E-03     0.26549E-06

And my topolhandmade.top

#include "ffoplsaa.itp"
#include "spc.itp"
#include "/home/martin/Desktop/gold/goldsf.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

Where do i make a misstake?

Cheers
	Martin