[gmx-users] Adding Hydrogens by pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 31 14:12:59 CET 2011

James Starlight wrote:
> exactly
> all hydrogens were represented as a part of the groupd in wich they 
> were. So is there possible way to explicit it?

I'm not quite sure I follow.  A united atom force field, by definition, does not 
have aliphatic hydrogens.  I suggest you consult the literature and understand 
the intrinsics of the chosen force field before you attempt to use it.

> Another question about pdb2gmx. about -term
> as I understood this must be used only if atoms for CAP groups are 
> presented in the PDB file mustnt it?

The -ter option can be useful in changing the protonation state of the termini 
or in adding caps.

> So what term exactly do? Doest it make a connection beetween CAP and C 
> and N termi or anothing else?

By default, pdb2gmx builds charged termini (NH3+ and COO-), per the typical 
protonation states of these groups in aqueous solution.  If a cap is present, 
then you don't want pdb2gmx doing that, so by choosing "None" for the termini in 
conjunction with the caps, only one proton is added to the N-terminus (as in an 
amide), and only one carbonyl oxygen remains on the C-terminus, such that the 
caps can be added in a sensible way.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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