[gmx-users] GROMACS AMBER DNA TERMINUS

[Maik Goette]

I guess you misunderstood that.
What you have there, is the terminal hydrogen, which is an hydroxyl one 
and therefore fully ok.
You should search for an atom at the nucleobase, which has atom type 25. 
This usually has to be changed. Strange error, though :)
I think its somewhere around N1 for guanines, e.g.

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/


Andreas Kukol wrote:
> Dear All,
> 
> I am using Gromacs 3.1.1 with the AMBER port. After following the 
> instructions on the ffamber web-page, pdb2gmx works fine. But according 
> to point 6:
> 
> "... However, for nucleic acids this also often causes pdb2gmx to 
> replace an H atom in the first residue of all nucleic acid chains with 
> an incorrect H atom, resulting in non-neutral charge. The correct atom 
> is generally replaced with an atom of type amberXX_25 (hydroxyl H), as 
> pdb2gmx treats it as a terminal hydrogen ..."
> 
> Indeed I find this atom in the first residue:
> 
> 1 amber99_25      1    DG5    H5T      1     0.4422      1.008   ; qtot 
> 0.4422
> 
> The solution given (a) is to correct the atom type and charge in the 
> .top file by hand.
> 
> My question is:
> What is the correct atom type and charge for this hydrogen ?
> 
> The ffamber03.rtp contains exactly this atom type and charge in the 
> specification for the residue DG5. So it should be correct ??
> 
> Many thanks
> Andreas
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