[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
> 
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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
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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>
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>                --         Bharat
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>                Room No. : 7202A, 2nd Floor
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>            --     ==============================____==========
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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)
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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>>
> 
> 
>     -- 
>     ==============================__==========
> 
>     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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