Hi Andy,
I did some work on molecular oxygen back in 2006. There have been a few
requests for molecular oxygen parameters so I decided to
dig them up. Here are the parameters that I used for that work. I leave it to you to read the relevant papers and decide if
these parameters are appropriate for your simulations.
Note that I went with an epsilon value that I converted myself from Fisher and
Lago (3.71000e-01) and considered
the value used by Marrink and Berendsen (3.63000e-01) to have been incorrectly
converted. However, we never did publish our
simulations so I can't give you a reference for that discrepancy, which, to my
knowledge, has not previously been reported.
After modifying the files as I outline below, you will need to rename your
oxygen residue and atomic names to match and then it
should respond properly to a run through pdb2gmx.
It probably makes a lot more sense to create an otwo.itp file, but I did this
in my early gromacs days and didn;t know how
to do that then. I am leaving the instructions intact as I did it at the time
since that is easier for me.
For a separate set of parameters, you might look at Bembenek and Rice JCP vol
113 #6 p. 2354-9 and Bembenek JCP 124 (2006).
I did not decide that the Fisher and Lago parameters were "better", I just
picked them since they had previously been used in our lab:
Al-Abdul-Wahid MS, Yu CH, Batruch I, Evanics F, Pomès R, Prosser RS. "A combined NMR and molecular dynamics study of the transmembrane
solubility and diffusion rate profile of dioxygen in lipid bilayers." Biochemistry. 2006 Sep 5;45(35):10719-28.
Although that paper utilized the values directly from Marrink and Berendsen.
## Add to ffX.atp:
; Added by Chris Neale March 16 2006 based on
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
OOT 15.99940 ; O in nitro R-NO2
## Add to ffX.rtp:
[ OTWO ]
; Added by Chris Neale March 16 2005 based on
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
[ atoms ]
OOA OOT 0.00 0
OOB OOT 0.00 0
[ bonds ]
OOA OOB
## Add to ffXbon.itp
; Added by Chris Neale March 16 2005 based on
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
[ bondtypes ]
; i j func b0 kb
OOT OOT 1 0.10160 659840.
;[ constrainttypes ]
;[ angletypes ]
;[ dihedraltypes ]
## Add to ffXnb.itp:
; Added by Chris Neale March 16 2006 based on
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
; name bond_type mass charge ptype sigma epsilon
OOT OOT 1 15.99940 0.000 A 3.09000e-01 3.71000e-01
Chris.
-- original message --
Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on
myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the
following
Fatal error:
Residue 'OXY' not found in residue topology database
I check the ff and I did not found the oxigen molecule.
I saw that somebody allready use this molecule in the mailing list:
On Tue, 18 Jun 2002, Valentin Gogonea
Is there a chance to contact him?
Is this molecule in any other ff?
How can I fix this?
How can I take the OXI and SO4 molecules out of my .pdb file without making
mistakes?
Hopping to be clear.
Thanks in advance
Andy
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