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

[Justin Lemkul]

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

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