[gmx-users] water overlaps gold bar

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Nov 29 21:57:42 CET 2006

> 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.

You need to increase the vdw radius for the gold atoms during that step,
which is in the vdwradii.dat, or something like that, in the directory
with all the ff files etc.

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