[gmx-users] Nucleic Acids -- Protonate ?

[Mark Abraham]

Viswanadham Sridhara wrote:
> Hello,
> 
> I wanted to perform MD simulation on a DNA structure I found from
> RCSB.org. After changing C, G, A, T to DCYT, DGUA, DADE and DTHY
> respectively, I used pdb2gmx to create topology file. It says missing
> hydrogens, which is obvious and I realized I could not use protonate
> command as ffgmx2.hdb does not have these residues to be protonated.
> Is there any other file to add missing hydrogens or Is there any other
> program which you can use to add missing hydrogens to nucleic acids.
> The total charge now is -43e, which is quite huge, and I am looking to
> see electric field effects on the DNA. This will be a lot of charge to
> neutralize by adding counter-ions, if I ignore hydrogens.

I don't know how to solve your problem, but merely adding counter-ions 
because you don't know where or how many hydrogens there might be is 
almost guaranteed to lead to a simulation that has no correlation with 
reality.

Mark