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,
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