[gmx-users] Adding new residue - modified LYS

[Dan Si]

Hi,



I'm struggling with adding a new residue to my MD simulation. I would like 
to create a residue (let's call it NML) that would be an original lysine 
(LYS) residue with methyl group attached to it's amide bond nitrogen. I'm 
using amber99sb-ildn force field for my simulations. Unfortunately, I'm very
new in using gromacs, so I would appreciate really !step-by-step! tutorial :
-) 




Do I need to perform QM calculation to obtain some of the parameters? If 
yes, should I use zwitter-ionic structure NH3-CH-(R)-C-(O)-O in the 
optimization?




I understand, I need to specify the topology of the new residue and 
parameters according to amber99sb-ildn force field, but how exactly am I 
suppose to do it? Which files I need to modify before running pdb2gmx and 
how?




Thank you very much for any answer! It will be extremely helpful for me...




Dan