[gmx-users] Umbrella sampling of phosphate ion binding
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 9 04:25:43 CEST 2011
bharat gupta wrote:
> Sorry to ask this ... If I try SMD with prodrug generated topology for
> the time being , will it be useful to do that ?? As I don't have much
> time as of now to parametrize and do SMD...
>
That's a great way to waste time. If you run a simulation with sub-par
parameters, you'll get questionable results. Any good reviewer would dismiss
work done with a lousy underlying model.
-Justin
> On Thu, Jun 9, 2011 at 10:42 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> bharat gupta wrote:
>
> Yes, I read the prodrug faqs... then in that case I have to
> parametrize
>
>
> So then you should know that the ADDHYD keyword solves your problem,
> right?
>
>
> the ion ... According to you there is no other way of doing it ??
>
>
> I didn't say there was no way to do it. It just won't be easy
> (assuming no one else has already developed them for your chosen
> force field - so spend some time in the literature). Read the
> primary reference for the force field you wish to use and derive
> suitable parameters accordingly. Plan on spending a fair bit of
> time doing this. Good parameters don't come easily.
>
> -Justin
>
> On Thu, Jun 9, 2011 at 10:30 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:
>
> 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>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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://ac.uk/prodrg/prodrg_faq.html>
> <http://ac.uk/prodrg/prodrg___faq.html
> <http://ac.uk/prodrg/prodrg_faq.html>>
>
>
> <http://davapc1.bioch.dundee.____ac.uk/prodrg/prodrg_faq.html
> <http://ac.uk/prodrg/prodrg_faq.html>
>
> <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>
>
> <http://www.gromacs.org/____Downloads/Related_Software/____PRODRG#Tips
> <http://www.gromacs.org/__Downloads/Related_Software/__PRODRG#Tips>>
>
> <http://www.gromacs.org/____Downloads/Related_Software/____PRODRG#Tips
> <http://www.gromacs.org/__Downloads/Related_Software/__PRODRG#Tips>
>
> <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>
>
> <http://www.gromacs.org/____Documentation/How-tos/____Parameterization
> <http://www.gromacs.org/__Documentation/How-tos/__Parameterization>>
>
> <http://www.gromacs.org/____Documentation/How-tos/____Parameterization
> <http://www.gromacs.org/__Documentation/How-tos/__Parameterization>
>
> <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>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto: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> <http://vt.edu>
> <http://vt.edu> | (540)
>
> 231-9080
>
>
> 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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>
>
> -- ==============================______==========
>
> 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>
> <http://vt.edu> | (540)
> 231-9080
>
> 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
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>
> -- ==============================____==========
>
> 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
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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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> --
> ==============================__==========
>
> 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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