[gmx-users] Ligand bond

abelius abelius at gmail.com
Thu Oct 20 12:06:05 CEST 2005


I've tried this tutorial before, but they don't make use of a covalently 
bond ligand. 
I was wondering if it were possible to add the ligand to the forcefield 
directly, but I'm not sure how to do that.
So, did you use your topology as an include without merging it to the 
topology create by pdb2gmx?


Andrea Carotti wrote:

> 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
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