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