Dear Users, In the gromacs manual on means to convert the pdb file to gromacs topology file I need to use pdb2gmx. Here I have to specify the force field .How to work with organic residues which do not exists . Since I had used general amber force field, and could not find this in the /share/top/ directory . Do I need to manually construct the .itp file for each residues. What will be the easiest way to construct a solvated box with user defined residues in gromacs.
Thanks Kirtana
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