[gmx-users] Bonds between P and O in bilayer head groups

[Mijiddorj Batsaikhan]

Dear Justin,

Thank you very much.


Best regards,

Mijiddorj

------------------------------
>
> Message: 4
> Date: Mon, 31 Oct 2016 18:58:29 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Bonds between P and O in bilayer head groups
> Message-ID: <19c7bf46-e498-4c88-8828-c2bebe4f5e3f at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 10/31/16 11:34 AM, Mijiddorj Batsaikhan wrote:
> > Dear gmx users,
> >
> > I want to simulate membranes system using gromacs v5. Initial structure
> was
> > built by Charmm-gui. Head groups' bonds between two O- and P are single
> in
> > the Charmm topology file as a following:
> >
> > ATOM H11B HAL2    0.09 !                      alpha4
> > ATOM P    PL      1.50 !        (-) O13  O12
> > ATOM O13  O2L    -0.78 !              \ /      alpha3
> > ATOM O14  O2L    -0.78 !               P (+)
> > ATOM O12  OSLP  -0.57 !              / \      alpha2
> > ATOM O11  OSLP   -0.57 !   (-) O14  O11
> > ATOM C1   CTL2   -0.08 !                 |     alpha1
> > ATOM HA   HAL2    0.09 !            HA---C1---HB
> > ATOM HB   HAL2    0.09 !                 |     theta1
> >
> > One of the them is double bond in the nomenclatures.
> >
> > (1) Which one is preferable for the simulation?
> >
>
> Double bonds in line drawings represent just one possible resonance form.
> You
> don't need to change anything about the topology because the chemical
> nature of
> this group is parametrized to account for equivalence among atoms.
>
> > (2) Are some metal ions needed near the head groups for the simulation?
>
> Condensation of ions around phosphate groups in membranes has been explored
> extensively with the CHARMM force field, particularly in the NBFIX terms
> assigned to some atoms and ions, to achieve a proper representation of
> these
> interactions.  You should read the papers conveniently cited in the CHARMM
> force
> field files that you're paraphrasing to understand what these interactions
> are
> and how they affect the physical properties of your membranes.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>