Andreas Kukol ak284 at cam.ac.uk
Sun Jan 7 19:13:25 CET 2007

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 

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

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