[gmx-users] Swissparam itp file

[neha bharti]

Hello all

I am trying to perform molecular dynamics simulation of ligand-protein
complex in popc lipid with charmm36 force field. I am taking help from Justin
A. Lemkul tutorial.

First I perform orientation of protein ligand complex by following command:

editconf -princ -f complex.gro -o complex_princ.gro
editconf -rotate 0 90 0 -f complex_princ.gro -o complex_princ_rotate.gro

Then after I separated the protein and ligand to generate their topology
file.
For protein pdb2gmx command is used for topology generation.
For ligand topology file swissparam is used after adding the hydrogen and
converting it to mol2 format.

But from swissparam I only get the .par and .rtf file in zip folder and
.itp is not persent. how to solve this issue??

Although when I use the ligand molecule without orientation (without
performing editconf -princ and editconf -rotate command) swissparam gives
the .itp file.
Can I use this itp file for oriented ligand molecule??

Please help