Dechang Li wrote: > Dear all, > > Sometimes,the PDB file contains water molecules which only have the > oxygen atom. Can > Gromacs add the hydrogen atoms of the water molecules?
No - you'll be better off deleting them all, re-solvating using genbox and then doing a normal minimization & equilibration process. An exception might be waters in an enzyme active site or such, in which case you're best off building the hydrogens by hand. > Additionly, when use Gromacs with the force field ffamber99, Can it add > the hydrogen > atoms of the DNA? Yes, if there are suitable hydrogen database entries in the relevant .hdb file. See chapter 5 of the manual for background here. > Can I use the force field ffamber99 to simulate the system which contains > proteins and DNAs? Check the contents of the .rtp file to see what "residues" are defined. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
