[gmx-users] Nucleic Acids -- Protonate ?

[Maik Goette]

 > 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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