On Mon, Apr 27, 2015, neha chaudhary wrote:
>
> I have used gromacs for protein-ligand simulation. then I extracted
> protein-ligand complex from rest of the system. Now I want to generate
> amber topology file (.inpcrd) file for the protein-ligand complex.
> What should I do for this?
This is done using LEaP, and a pdb-format file containing the coordinates of
your protein-ligand complex. Assuming that you wish to use the Amber force
fields, the fact the you used gromacs in an earlier stage is more or less
irrelevant. Just follow the tutorials for setting up systems, esp. tutorials
B0 and B4.
...dac
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Received on Mon Apr 27 2015 - 05:00:03 PDT
