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

servaas michielssens servaas.michielssens at student.kuleuven.be
Wed Jun 11 12:07:58 CEST 2008

If you have amber, you can make your topology in amber and convert them to 
gromacs with the script on this website:


kind regards,


> 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, 

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