[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>>
> 
>            ==============================____==========
>            --     gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>            <mailto: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 at gromacs.org>
>            <mailto:gmx-users-request at __gromacs.org
>         <mailto: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>
>         <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>
> 
>     ==============================__==========
>     -- 
>     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>
>     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
>     <mailto: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 <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

========================================



More information about the gromacs.org_gmx-users mailing list