Hi, I have a question regarding to using forcefield amber99 in Gromacs. I have all the parameter files of amber99. I am doing the MD of carbon nanotube with DNA. I have changed the .pdb file of the DNA according to the instruction. I generated the topology of DNA with identifying -water tip5p.gro. The topology file of DNA is also generated successful. Pymol is used to visualize the DNA structure. Now, I am doing the energy minimization. When I use the grompp command, the output is that "Fatal error: No such moleculetype SOL". I am wondering can anybody tell me how to use the tip5p model of water.
Also, actually, I want to do the simulation with tip3p. But I could not find tip3p.gro. I checked back. There was also another person asked the same question. But, I don't quite following the answer. Do you minding telling me more about the process?
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