[gmx-users] Umbrella sampling of phosphate ion binding
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 9 03:30:14 CEST 2011
bharat gupta wrote:
> I found it in the /shared/top/ gmx.ff folder . Here's the file
>
> ;
> ; Force field based on GROMOS with new charges as described in
> ; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
> ; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
> ; mottle virus coat protein in solution with phosphate ions
> ; Biophys. J. 71 pp. 2920-2932 (1996)
> ;
> [ moleculetype ]
> ; name nrexcl
> h2po4 4
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> ; use charges from Janez Mavri
> 1 OA 1 PI O1 1 -0.777
> 2 OA 1 PI O2 1 -0.777
> 3 OM 1 PI O3 1 -0.943
> 4 OM 1 PI O4 1 -0.943
> 5 P 1 PI P 1 1.596
> 6 HO 1 PI H1 1 0.422
> 7 HO 1 PI H2 1 0.422
>
> [ bonds ]
> ; ai aj funct c0 c1
> 5 1 1 1.637000e-01
> 5 2 1 1.637000e-01
> 5 3 1 1.478000e-01
> 5 4 1 1.478000e-01
> 6 1 1 0.943000e-01
> 7 2 1 0.943000e-01
>
> [ angles ]
> ; ai aj ak funct c0 c1
> 2 5 1 1 1.015000e+02 400
> 3 5 1 1 1.059000e+02
> 4 5 1 1 1.082000e+02
> 3 5 2 1 1.059000e+02
> 4 5 2 1 1.082000e+02
> 4 5 3 1 1.248000e+02
> 6 1 5 1 1.082000e+02
> 7 2 5 1 1.082000e+02
>
> [ dihedrals ]
> ; ai aj ak al funct
> 6 1 5 2 1
> 7 2 5 1 1
>
> Can I use it or not ??
>
Not likely. Please read in the manual about why the gmx.ff force field should
not be used.
-Justin
> On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> bharat gupta wrote:
>
> does the gromacs force field has topology and ff parameter for
> H2PO4(-) ion . As I have derived both topology and FF parameter
> from prodrug
>
>
> Probably not; check the .rtp file for your desired force field.
>
>
> server and after checking the topology I found that it has
> deleted of the hydrogen.
>
>
> See the PRODRG FAQ; this gets asked all the time.
>
> http://davapc1.bioch.dundee.__ac.uk/prodrg/prodrg_faq.html
> <http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html>
>
> No matter what PRODRG gives you, the charges will probably be
> useless anyway:
>
> http://www.gromacs.org/__Downloads/Related_Software/__PRODRG#Tips
> <http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips>
>
> So you're in for the difficult process of parameterization if no
> one's already developed parameters for your molecule:
>
> http://www.gromacs.org/__Documentation/How-tos/__Parameterization
> <http://www.gromacs.org/Documentation/How-tos/Parameterization>
>
> -Justin
>
> On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> bharat gupta wrote:
>
> Hi Justin,
>
> I am having following doubts regarding umbrella sampling of
> phosphate ion binding to my protein .
>
> 1. As per the tutorial, I need to fix an immobile
> reference. In
> my case which region do I have to fix as my protein
> consists of
> one single chain. Since I am studying the binding and
> unbinding
> of ion, shall I fix the ion fixed. If it's so, then do I
> have to
> give a different chain name for it as my complex doesnot
> chain
> name for ion/ligand.
>
>
> You don't need an immobile reference just because my tutorial
> did.
> I had a particular need to do so. For your purpose, I
> highly doubt
> it's necessary. You're looking at small molecule-protein
> interactions, not protein-protein interactions.
>
>
> 2. What should be the size of box and how do I know where to
> place the protein's COM in box (the precise location).
>
>
> The absolute COM is somewhat irrelevant; all distances during
> pulling are relative. You can place the protein in a certain
> location in the box for convenience if you like. The box
> size must
> be greater than twice the pull distance, as explained in the
> tutorial. The amount that you wish to pull will dictate both the
> location of the protein and the box size.
>
> -Justin
>
> -- ==============================____==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
> <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
>
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> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
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> <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
>
>
> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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