[gmx-users] Deuterate, heavyh options inconsistent (was: Water molecules cannot be settled, why?)

[Ladasky]

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?

I can post my PDB and MDP files, and my sequence of commands, if anyone
wants to reproduce my results.




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