[gmx-users] Nucleic Acids -- Protonate ?
Mark.Abraham at anu.edu.au
Mon Feb 12 01:04:25 CET 2007
Viswanadham Sridhara wrote:
> 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
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