[gmx-users] Bonds between P and O in bilayer head groups
b.mijiddorj at gmail.com
Tue Nov 1 07:42:08 CET 2016
Thank you very much.
> 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
> > built by Charmm-gui. Head groups' bonds between two O- and P are single
> > 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.
> 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
> interactions. You should read the papers conveniently cited in the CHARMM
> field files that you're paraphrasing to understand what these interactions
> and how they affect the physical properties of your membranes.
> 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
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