[gmx-users] GROMACS AMBER DNA TERMINUS

[Erik Marklund]

_______________________________________________
Erik Marklund, PhD student
Laborarory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, 	Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

On Sun, 7 Jan 2007, 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 ?
>

Try what's suggested on the website just before solution (a), namely to 
examine the difference between using aminoacids.dat and aminoacids-NA.dat. 
That worked just fine for me (Actually, I used solution (b), but I 
checked the results using the aforementioned method as fas as I 
remember.)

/Erik

> 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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