On 2/6/17 1:15 PM, Mahboobeh Eslami wrote:
On Monday, February 6, 2017 11:59 AM, Mahboobeh Eslami
<mahboobeh.esl...@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.ne...@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-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul
<jalem...@vt.edu>
Sent: 05 February 2017 11:18:10
To: gmx-us...@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
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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