[gmx-users] Ligand bond

[Andrea Carotti]

Hi Abelius and Tserjk,
I will explain my modus-operandi:
in similar situation I've linked (using the specbond.dat file) the proper 
atoms, then I've completed manually the topology file created using the 
gromos book,
infact some parameters (like angles,bond and dihedrals) are missing.
If you want a very good tutorial about drug-enzime complex is here
http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
For the perl module, sincerely I don't know nothing about that.
Bye
Andrea