On 7/27/12 9:55 PM, Ladasky wrote:
Hello Mark,
Thanks for your reply. It has taken me several days to make some progress
on my issues. I'm just going to address one specific point in this post.
Mark Abraham wrote
On 19/07/2012 6:52 PM, Ladasky wrote:
I once used the -deuterate option in pdb2gmx, and I am presently trying
to avoid it. I asked whether -deuterate has any effect on water
molecules
in a previous post, or only on the hydrogens in proteins. So far, I have
not been made to understand that genbox silently deuterates water
hydrogens,
if it receives a deuterated protein as input.
Probably. You'd have to inspect the atom types in the resulting
processed topology (e.g. from grompp -pp) to be sure.
I have now had a chance to look at this issue. I generated a small,
tri-peptide protein, and solvated it in a small box of solvent. I tried
pdb2gmx once in default mode for hydrogen atoms, once with the -deuterate
option, and once with the -heavyh option. I looked at the topology files
produced by grompp -pp.
Excerpt of grompp_1.top (pdb2gmx default, normal hydrogen):
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 ALA rtp ALA q +1.0
1 NL 1 ALA N 1 0.129 14.0067 ; qtot
0.129
2 H 1 ALA H1 1 0.248 1.008 ; qtot
0.377
(snip)
; Include water topology
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 SOL OW 1 -0.82 15.99940
2 H 1 SOL HW1 1 0.41 1.00800
3 H 1 SOL HW2 1 0.41 1.00800
Here are the same parts of grompp2.top, generated using the -deuterate
option in pdb2gmx. Protein hydrogens have increased mass. Solvent
hydrogens DO NOT have increased mass. Heavy atoms to which deuterated
hydrogens have been attached do not have reduced mass.
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 ALA rtp ALA q +1.0
1 NL 1 ALA N 1 0.129 14.0067 ; qtot
0.129
2 H 1 ALA H1 1 0.248 2.016 ; qtot
0.377
; Include water topology
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 SOL OW 1 -0.82 15.99940
2 H 1 SOL HW1 1 0.41 1.00800
3 H 1 SOL HW2 1 0.41 1.00800
Finally, here the same parts of grompp4.top (pdb2gmx -heavyh option). This
time, solvent hydrogens ARE given an increased atomic weight, and the
solvent oxygen is reduced in atomic weight to make up the difference. In
the protein, the mass of the heavy atom to which hydrogens attach is also
reduced.
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 ALA rtp ALA q +1.0
1 NL 1 ALA N 1 0.129 4.9347 ; qtot
0.129
2 H 1 ALA H1 1 0.248 4.032 ; qtot
0.377
; Include water topology
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 SOL OW 1 -0.82 9.95140
2 H 1 SOL HW1 1 0.41 4.03200
3 H 1 SOL HW2 1 0.41 4.03200
This was in fact the concern that occurred to me when I abandoned the use of
-deuterate. I wondered about the consequences of changing the atomic weight
of hydrogen. I wondered further about the unrealistic nature of a
heterogenous system, with some normal-mass hydrogens and some heavy
hydrogens. As I did not see any option for adjusting the solvent hydrogen
mass, I assumed that the system would be mixed, and I was right.
It was stranger still to see that the -heavyh option, which I've never used,
DOES alter solvent hydrogen masses, to make a uniform system.
Are these two distinct behaviors what GROMACS users want? Or did I just
uncover a bug?
These are distinct behaviors by design. The use of heavy hydrogens (4x mass) is
used in cases where one might want to increase the time step. This is described
in the last paragraph of the pdb2gmx help info. Deuteration is carried out on
the solute with which pdb2gmx is presented; if one wants to model D2O, one needs
a suitable parameter set for it. I suspect it exists somewhere, but have never
had a need to go looking for one myself.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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