Previous Thread
Next Thread
Print Thread
Page 1 of 2 1 2
Parameters for molecular Oxygen
#28482 10/19/11 04:50 PM
Joined: Oct 2011
Posts: 10
S
shrek Offline OP
Forum Member
OP Offline
Forum Member
S
Joined: Oct 2011
Posts: 10
Hi.

I am a bit new to the forums and to CHARMM, so please accept my apologies if the questions are very naive. I had a query regarding the parametrization of the Molecular Oxygen in the paper: " Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics" by Wang et al.

Here the paper discusses the parametrization of free molecular Oxygen (As opposed to the heme O2) but does not suggest the atomtype used for the parametrization. I was wondering which atomtype was to be used especially considering for the non-bonded pairwise interactions. If any one can help me regarding this, it would be great!

There have been a couple of discussion earlier on the forums regarding this parametrization without a concrete outcome, although this article was not brought up there.

Thanks in advance!

Re: Parameters for molecular Oxygen
shrek #28483 10/19/11 05:41 PM
Joined: Sep 2003
Posts: 8,425
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,425
For different values of epsilon and Rmin/2, a new atom type would be required; you should not use an existing atom type.


Rick Venable
computational chemist

Re: Parameters for molecular Oxygen
rmv #28487 10/20/11 09:02 AM
Joined: Oct 2011
Posts: 10
S
shrek Offline OP
Forum Member
OP Offline
Forum Member
S
Joined: Oct 2011
Posts: 10
Thanks for the reply RMV.

And of course not. I won't be using an existing atom type unless it has been validated for that purpose. I was interested in knowing if there was an alternate atom-type as suggested by the paper I linked.

Re: Parameters for molecular Oxygen
shrek #28490 10/20/11 02:28 PM
Joined: Sep 2003
Posts: 8,425
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,425
Then why did you ask the question if you knew the answer?


Rick Venable
computational chemist

Re: Parameters for molecular Oxygen
rmv #28493 10/20/11 02:52 PM
Joined: Oct 2011
Posts: 10
S
shrek Offline OP
Forum Member
OP Offline
Forum Member
S
Joined: Oct 2011
Posts: 10
My mistake. Can you tell me what combination rules are there for CHARMM? I can then create my own atom-type for O2.

Re: Parameters for molecular Oxygen
shrek #28500 10/20/11 07:24 PM
Joined: Sep 2003
Posts: 8,425
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,425
The parameters in the supplementary material of that paper are given in a form that can be directly used in CHARMM. You just have to pick a chemical name and integer atom type number that are unique for the MASS statement, and add the epsilon and Rmin/2 values in the NONBOND section of the parameter file.

As noted in the 2009 CHARMM paper, by default Rmin/2 values are averaged arithmetically, and epsilon is averaged geometrically; there is support for other combining rules.


Rick Venable
computational chemist

Re: Parameters for molecular Oxygen
rmv #28502 10/21/11 02:16 AM
Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
I have some reservations about those parameters, though. If I interpret the table correctly, the nonzero charges for the "explicit gas diffusion simulation" are taken from heme oxygen. For free oxygen, this seems unphysical. The LJ parameters, on the other hand, are not the same as in toppar_all22_prot_heme.str ; they are from TIP3P , so they used charges from one irrelevant model with LJ parameters from another one...

For the "implicit ligand sampling", they used the correct heme oxygen LJ parameters and set the charges to 0. Yet, the original heme oxygen LJ were transfered from carbonyls in the protein force field, which might not work for free triplet oxygen. Contrary to commonly drawn lewis structures, the O-O bond is not a double bond, and the species has an unusual electronic structure.

Both models, especially the second one, feature O-O distances that seem too short compared to the reference value of 1.23 in toppar_all22_prot_heme.str and the experimental value of 1.207 for ground state (triplet!) oxygen.

Then again, I don't know of any well-validated parameters for free oxygen in solution. Generating them would be a more challenging endeavor than it seems. In the end, it may not matter that much; in practice, a nonpolar blob of approximately the right size would probably yield qualitatively correct results, though for quantitative free energy calculations, more validation would be required at the least.

Oh yeah, apart from the above reservations, I don't see any objection to using an existing atom type that has the same LJ parameters.

Re: Parameters for molecular Oxygen
Kenno #28503 10/21/11 02:58 AM
Joined: Sep 2003
Posts: 8,425
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,425
It sounds like just a new O2 residue with the charges set to zero may be sufficient, in that case. I hadn't noticed that their zero charge model used the same eps and Rmin/2 as the slightly polarized heme O2.


Rick Venable
computational chemist

Re: Parameters for molecular Oxygen
Kenno #28513 10/21/11 01:53 PM
Joined: Oct 2011
Posts: 10
S
shrek Offline OP
Forum Member
OP Offline
Forum Member
S
Joined: Oct 2011
Posts: 10
Thanks Kenno and RMV. I guess that's a good first approximation. I will try to validate the results with some partition coefficients. But right now, starting with HEME Oxygen with its charges set to zero would be my starting structure.

EDIT: Or should I use the TIP3 oxygen VDW parameters? I am confused again.

Last edited by shrek; 10/21/11 01:54 PM.
Re: Parameters for molecular Oxygen
shrek #28514 10/21/11 02:50 PM
Joined: Sep 2003
Posts: 8,425
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,425
I would use the heme OM type, since it is for an O2 molecule.


Rick Venable
computational chemist

Page 1 of 2 1 2

Moderated by  alex, chmgr, John Legato 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.010s Queries: 35 (0.004s) Memory: 0.9845 MB (Peak: 1.1162 MB) Data Comp: Off Server Time: 2020-04-10 06:17:00 UTC
Valid HTML 5 and Valid CSS