> 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. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
