[MMTK] Dynamics with specific distance constraint

Jean Didier Pie Marechal JeanDidier.Marechal at uab.cat
Fri Apr 16 13:54:21 UTC 2010


Dear Konrad,

I'd like to perform a series of MD runs on some peptides with distant contraints between several atoms. I guess MMTK allows to add one or more constraints but can't find out how.

On the other side, I am trying to get to the examples at http://dirac.cnrs-orleans.fr/Manuals/MMTK/MMTK_9.html but none of the link functions ( at least for )me. Any idea what this could be due to?

All the best,
JD

Dr. Jean-Didier Maréchal
Lecturer
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: mmtk-request at starship.python.net
Data: Dimarts, Abril 13, 2010 2:00 pm
Assumpte: mmtk Digest, Vol 81, Issue 2

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> Today's Topics:
> 
>   1. Solvation of the protein hemoglobin (prabhakar g)
>   2. Re: Solvation of the protein hemoglobin (Konrad Hinsen)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Tue, 13 Apr 2010 10:05:07 +0900
> From: prabhakar g <prabha.iisc at googlemail.com>
> Subject: [MMTK] Solvation of the protein hemoglobin
> To: mmtk at starship.python.net
> Message-ID:
> 	<p2t9b3591c11004121805x8dbad5e2ke23934a68bbb0009 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi,
> 
> Thank you Dr.Konrad, my study relates to simulation of the protein
> hemoglobin and its hydration layer.
> 
> But perhaps what you want is to take the protein and 
> crystallographic water
> from a PDB file, put it into a larger periodic system, and add lots of
> solvent. In that case, the example script to look at is
> Examples/MolecularDynamics/
> >
> > solvation.py.
> 
> 
> Yes I tried to solvate a molecule of hemoglobin using the solvate 
> plugin (
> http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/)  provided 
> with the
> vmd. In case of  hemoglobin there is an inter subunit pocket in 
> between the
> four chains of hemoglobin ( stretching approximately to about 10
> angstroms).  When i solvate the molecule, this pocket is completely 
> filledwith water molecules.
> 
> But when I happen to check with one of the crystal structures 
> (2HHB) of
> hemoglobin, this pocket of hemoglobin was sparsely populated with 
> watermolecules.  Sir my question are:
> 
> 1.Does solvating the structure for simulations place more number of 
> watermolecules  around and in the pocket of the protein molecule 
> than observed in
> the physiological conditions.
> 
> 2.Is it possible to know probability of the  the inter subunit 
> pocket being
> completely filled with water molecules in physiological conditions, in
> protein solutions.
> 
> 3. What are the methods could one use to solvate the protein close 
> to the
> realistic physiological conditions.
> 
> could anyone please give some suggestions.
> 
> Sincerely
> prabha
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> ------------------------------
> 
> Message: 2
> Date: Tue, 13 Apr 2010 08:12:22 +0200
> From: Konrad Hinsen <research at khinsen.fastmail.net>
> Subject: Re: [MMTK] Solvation of the protein hemoglobin
> To: mmtk forum <mmtk at starship.python.net>,	prabhakar g
> 	<prabha.iisc at googlemail.com>
> Message-ID:
> 	<1536BCF6-463E-4787-984B-4DE38F97BB30 at khinsen.fastmail.net>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes
> 
> On 13 Apr 2010, at 03:05, prabhakar g wrote:
> 
> > But when I happen to check with one of the crystal structures 
> (2HHB)  
> > of hemoglobin, this pocket of hemoglobin was sparsely populated 
> with  
> > water molecules.  Sir my question are:
> >
> > 1.Does solvating the structure for simulations place more number 
> of  
> > water molecules  around and in the pocket of the protein molecule 
> 
> > than observed in the physiological conditions.
> 
> Yes. However, in the case of crystallographic water molecules, the  
> problem is in the observation rather than in the simulation.  
> Crystallography can observe only the most stable water molecules, 
> the  
> ones that are in nearly the same position in all copies of the unit 
> 
> cell. Crystallographic waters molecules thus always represent only 
> a  
> small subset of solvent molecules.
> 
> > 2.Is it possible to know probability of the  the inter subunit  
> > pocket being completely filled with water molecules in 
> physiological  
> > conditions, in protein solutions.
> 
> As far as i know, no. There aren't many experimental techniques 
> that  
> are sufficiently sensitive to water molecules to provide this kind 
> of  
> detail. Perhaps some clever trick with something like neutron  
> scattering on a carefully deuterated sample could do it.
> 
> > 3. What are the methods could one use to solvate the protein 
> close  
> > to the realistic physiological conditions.
> 
> That's impossible to say before someone has found a way to  
> characterize the physiological conditions with more certainty. If 
> you  
> want to be realistic, you have to take into account not just 
> waters,  
> but ions and other small molecules that are present around 
> proteins. I  
> don't know of any experimental technique that would give you the  
> information you need.
> 
> Konrad.
> --
> --------------------------------------------------------------------
> -
> Konrad Hinsen
> Centre de Biophysique Mol?culaire, CNRS Orl?ans
> Synchrotron Soleil - Division Exp?riences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: research at  khinsen dot fastmail dot net
> --------------------------------------------------------------------
> -
> 
> 
> 
> 
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