[gmx-users] GROMACS AMBER DNA TERMINUS
ak284 at cam.ac.uk
Sun Jan 7 19:13:25 CET 2007
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 ??
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