Dear gromacs users,
I have a quetion regarding using amber forcefield in gromacs.
I did the DNA and water interaction simulation. After the energy
minimization, the
original helix-structured DNA becomes two fragments. At this stage,
I assume that the simulation process is correct.
I used exactly
You want to name the atoms according to the atom types in ffamberXX.rtp
file. For an example of this for DNA see the dickerson.pdb provided in the
README directory of the ffamber port or this pdb can be downloaded on its
own from:
http://folding.stanford.edu/ffamber/
Tom
--On 30 May 2007
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