[gmx-users] Nucleic Acids -- Protonate ?

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 12 07:14:28 CET 2007

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 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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