[gmx-users] converting pdb of protein+ATP+water+ion into gromacs files

Dina Mirijanian dmirij at brandeis.edu
Wed Oct 23 22:28:54 CEST 2013

I am trying to convert a protein+ATP+water+ion system pdb into gromacs
files.  I need to use the existing water and ion coordinates.  I can
convert the protein part using pdb2gmx and grompp fine.  But, I do not know
how to process the solvent and ion coordinates separately and combine them
to make the final system.  Can anyone give me direction?  I am new to
Thanks you very much.

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