[gmx-users] system contains proteins and DNAs with ffamber99

If you have amber, you can make your topology in amber and convert them to gromacs with the script on this website: http://chemistry.csulb.edu/ffamber/tools.html kind regards, servaas Dear all, Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can Groma

Re: [gmx-users] system contains proteins and DNAs with ffamber99

Dear Dechang, in ff03 forcfield the nucleic acid parameters are the same as in the ff99. But ff99 forcefield for proteins is not the best choice due to it's 'helix friendly'nature. A better choice is to choose the ff03 forcfield for protein and dna, as well. hoe this helps. Balazs Mark Abraham írt

Re: [gmx-users] system contains proteins and DNAs with ffamber99

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 mo

Re: [gmx-users] system contains proteins and DNAs with ffamber99

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 & eq

[gmx-users] system contains proteins and DNAs with ffamber99

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 ffa