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

[servaas michielssens]

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
> 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,