[gmx-users] modelling of calcium ions

[Justin Lemkul]

On 2/6/17 1:15 PM, Mahboobeh Eslami wrote:
>
>
>      On Monday, February 6, 2017 11:59 AM, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
>
>
>  Hi
> Thank you for your answersI want to change ffnonbonded.itp file for calcium ions. Have nm and KJ/mol units been used for sigma and epsilon values in this file, respectively? I ask this question to ensure.Thank you so much

Yes.  See Chapter 2 of the manual for the units GROMACS uses for everything.

-Justin

> Best wishes
>
>
>     On Sunday, February 5, 2017 9:29 PM, Christopher Neale <chris.neale at alum.utoronto.ca> wrote:
>
>
>  The things you'll have to be most careful of include whether the calcium ion parameters you choose can get the correct coordination states (as I recall, Calcium's coordination can be quite variable experimentally, in contrast to something like magnesium, which has a more strict coordination number). You can check this possibly by putting a calcium ion in water and integrating the RDF over the first shell, etc (or, obviously reading the literature about simulations with those ca2+ parameters). In addition, you might have to think about getting the right chi rotamers of asn and gln if they assist coordination (they are not always correct in crystal structures) and protonation states of coordinating side chains. For example, I am not sure if His can help to coordinate calcium, but if it can then you'll want to have the right tautomer (protonation on the epsilon vs delta nitrogen atom), etc.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: 05 February 2017 11:18:10
> To: gmx-users at gromacs.org; Mahboobeh Eslami
> Subject: Re: [gmx-users] modelling of calcium ions
>
> On 2/5/17 4:18 AM, Mahboobeh Eslami wrote:
>> Hi all GMX usersI hope you are wellI want to simulate a protein-ligand complex. There are two calcium ions in the crystallographic structure of protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I use these parameter for modelling of calcium ions.? Please guide me.ThanksBest
>>
>
> Ca2+ is already present in every force field in GROMACS.  pdb2gmx should handle
> it out of the box as long as the residue is named appropriately.  If you have
> (good) reason to change any aspects of the parameters, you'll have to alter
> ffnonbonded.itp to change the attributes of the corresponding atom type.
>
> -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
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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-- 
==================================================

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

==================================================