[gmx-users] RE: Bound oxygen molecule

[Gia Maisuradze]

Hi,

I am working on dimeric hemoglobin, which has a bound oxygen molecule O2. 
When I convert pdb file to gro and top files by pdb2gmx it fails, since 
Gromacs does not recognize O2. I have checked the discussion list and this 
kind of question was asked once, however, I still have the couple questions 
about that. As I understood from previous discussion it was suggested to 
consider oxygen molecule to be covalently bound to the iron, which means in 
pdb file in residue column I changed O2 by HEM. But the conversion from pdb 
to gro fails again, because HEM joined with oxygen is not supported by 
gromacs. Although the conversion was failed I still got .itp files which do 
not include molecular oxygen. My question is following: should I change 
these itp files obtained after failure by adding information about bonds, 
angles, etc. for molecular oxygen  or go to the ffxxxbon.itp file and add 
bonds, angles, dihedrals for molecular oxygen and then perform the 
conversion? If anybody already have the topology for this case, I would 
appreciate to know what parameters (e.g. force constants) were used.

Thanks in advance,
Gia