I have to simulate a big complex with two different proteins, GNP ligand and acetate(ACT), MG and CA ions.
I’m using gromacs software and amber force field to generate the topology for the protein.
I have faced a first issue regarding ACT ion and GNP ligand because they are not found in residue topology database. But I guess AMBER supports this molecule inherently.
For that, I have used PRODRG program to generate the GNP topology first and I have followed the same procedure as explained in Benvan Lab tutoriel.
The structure I got from this phase is good but when I tried to superpose the GNP with my reference structure it seems that the built GNP coordinates are not the same. The GNP is translated.
My first question is: is PRODRG the suitable program for generation of small molecule topologies?
Should I look at the atomic charges obtained with PRODRG for GNP before merging it with the protein?
Could any on, please, suggest me other ways to succeed this critical phase.