1] I want to solvate a protein with ammonia , how can i do it? Is there ammonia .gro/ammonia.pdb file available.?
2] How can i solvate with a mixture of solvents > eg., ammonia and water...??
Sayantan Mondal
You have to create a topology file (***.itp) for ammonia and a ***.pdb file containing single ammonia.
In your ***.top file write
#include ***.itp.
Then, use genbox /gmx solvate command with -ci and -nmol flags to insert required number of ammonia molecules.
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