Hi Stéphane, 

Thanks for your reply. The complex is a glycated amino acid (a derivative of glucose covalently bound to the amine group of lysine). 

How does parmchk2 know which parameters to pick from? 

What do you mean by the "conversion rules given in other AMBER force fields available in the current gromacs distribution"? I have the amber force fields which come with Gromacs, obviously, but I've never seen a conversion rule before. 

Would it not be more rigorous it the values we calculated using ab initio techinques (HF/6-31+G I believe is what Amber used) rather than an approximation? 

I appreciate your help. 

ALSO: I forgot to mention, this particular structure has no database entry. It exists in theory. My group is trying to purify it at the moment. 

Anthony

You can use coot for building missing structure (amino acids).

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Hi Navneet, 

Thank you for that suggestion, I will certainly look into it. However, I have a feeling that Coot will not derive partial charges for gromacs charge groups using an amber force field nor will it derive force constant and equilibrium bond distances. 

I think some tools in coot like "real space refine zone" and "regularize zone" will fix all the addition and changes you do with your structure.

No idea about Amber ff but I used earlier with gromos ff .

Hi Stéphane, thanks for all of that information. There is certainly a lot there. 

I've been using Gromacs for about five years now, but I'm a complete novice at Amber. 

Thanks again.