[gmx-users] Umbrella sampling of phosphate ion binding
bharat gupta
bharat.85.monu at gmail.com
Thu Jun 9 03:40:06 CEST 2011
Yes, I read the prodrug faqs... then in that case I have to parametrize the
ion ... According to you there is no other way of doing it ??
On Thu, Jun 9, 2011 at 10:30 AM, Justin A. Lemkul <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>> 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://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>
>> >
>>
>> 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>
>> >
>>
>> -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://vt.edu/Pages/Personal/justin>
>> >
>>
>> <http://www.bevanlab.biochem._**_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
>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>> <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
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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://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
>> 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<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
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