[gmx-users] Hi ..

[Mark Abraham]

Navratna Vajpai wrote:
> Dear All 
> I have been able to carry on with the MD run of my peptides. But when I 
> converted the traj into the pdb file I realized that there are no HA 
> atoms in the pdb. I checked the rtp file and found that even those atoms 
> are not defined there. So can anyone tell me how to get the HA (after or 
> before the MD run) as i need them explicitly . I was trying to look for 
> the options available in the trjconv but could not find.
> Thanks and regards

Does your force field include explicit non-polar hydrogen atoms? Or does 
it use united atoms?

Mark