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
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