[gmx-users] Nucleic Acids -- Protonate ?

[David van der Spoel]

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.
> 
> Looking foward to your response.
> 
> Best Regards,
> Vissu
> 
Do not ever use ffgmx2 or ffgmx!

Download the amber force field from folding.stanford.edu/ffamber and 
*carefully* follow their instructions for simulating DNA.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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