[gmx-users] Umbrella sampling of phosphate ion binding
bharat gupta
bharat.85.monu at gmail.com
Thu Jun 9 03:28:38 CEST 2011
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 ??
On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul <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>> 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> | (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>
>> >
>>
>> ==============================**__==========
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>> Please search the archive at
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>
>> Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>
>>
>> --
>> 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>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
--
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110609/308f2ec3/attachment.html>
More information about the gromacs.org_gmx-users
mailing list