I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.
My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use because there isn't an entry in .rtp.
use following topology
# include {nonbonded force field file e.g. ffmgxnb.itp}
# include { bonded force field file e.g. ffgmxbon.itp }
# include { your molecule.itp }
[ system ]
[ molecules ]
or
add the molecule in the .rtp file and run pdb2gmx.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
(Commenting on Rakesh Gupta's answer, which is largely correct.) For modern versions of gromacs, the force fields are included as:
#include "amber99sb-ildn.ff/forcefield.itp"
Also note that using the gmx force field is strongly discouraged.
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