[gmx-users] Nucleic Acids -- Protonate ?

Viswanadham Sridhara muta.mestri at gmail.com
Mon Feb 12 00:36:41 CET 2007


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,

Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.

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