[gmx-users] miscelle formation using ligands only

Chetan Puri chetanpuris at gmail.com
Sat Sep 12 05:59:28 CEST 2015

I am using gromacs for the first time . I have installed gromacs 5.0.4
version and i want to check a miscelle is formed or not using 5 different
 ligands in different ratios. I have gone through all basic tutorials on
how to use gromacs ( lysosyme,protein-ligand).

But i am stuck with the problem of having ligands only for simulation due
to no force field and topology file.
                      I have tried to use packmol to pack a cubic box with
all my different ligands in different ratios and generated a pdb file but
without making a topology file i am stuck.
          So if some one can suggest some possible ways  of doing it and i
don't have much computational background of manipulating various file
extensions of gromacs.

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