[gmx-users] Nucleic Acids -- Protonate ?

[Viswanadham Sridhara]

Thanks Mark, David, Yang, Joern and Maik for your suggestions. Now the
only way I see is to use amber forcefield for nucleic acid
simulations.

Regards,
Vissu.

P.S. : **keywords : Nucleic Acids, DNA, RNA, Gromacs, AMBER FF, MD simulations


On 2/12/07, Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:
>  > 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.
>
> The answer to the problem has been presented (amber FF port), but I
> thought exactly the same...and btw...Mark, the one with the car mechanic
> was great...;)
>
> Best regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>         mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> Mark Abraham wrote:
> > 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
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-- 
Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.