[gmx-users] Problems with forcefield amber99 in Gromacs
suriayang at gmail.com
Sat May 26 00:24:49 CEST 2007
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
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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