[gmx-users] Ligand in PRODRG server is protonated. Why?

[Andrew Bostick]

Dear gromacs users,

I am doing MD simulation of protein-ligand complex. For ligand, I used
PRODRG server.

My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of
Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In
PRODRG outputs, ligand is protonated on N atom and has 1 atom more than
original structure (58 atoms). I don't want this output. My aim is studying
unprotonated structure of Tamoxifen.

How to resolve that.

Best,
Andrew