hi, I think the answer to both of your questions is YES! Though, I have used ffamber03 for simulating protein+DNA. But I guess it shouldn't matter.
Regards, Vignesh On Wed, Jun 11, 2008 at 3:50 PM, Dechang Li <[EMAIL PROTECTED]> 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? > > Additionly, when use Gromacs with the force field ffamber99, Can it add > the hydrogen > atoms of the DNA? Can I use the force field ffamber99 to simulate the > system which contains > proteins and DNAs? > > > > Best regards, > > > > ========================================= > Dechang Li, PhD Candidate > Department of Engineering Mechanics > Tsinghua University > Beijing 100084 > PR China > > Tel: +86-10-62773779(O) > Email: [EMAIL PROTECTED] > ========================================= > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" "The rewards of sincere resolves are highs money can never buy!"
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