[gmx-users] ligands bound to a surface

[Daniel Rigden]

Hi again

Thanks, I now see that it will be possible to simulate the attachment of the ligands to the surface 
by contraining the x-coordinate (for example) of the bound atom.  However, there's another
potential issue I just thought of.

The ends of the ligands are away from the surface, exposed to solvent.  The system would
therefore be put in a solvent box. But the solvent should not be allowed to reappear at the
surface side of the box, x=0, when it leaves the box at x=box length.  Is it possible to 
turn off this behavious selectively for one face of the box?  Or what I have to include an
explicit surface to prevent this happening?  Could I simply place a 2D array of atoms at
x=0 and fix their positions using big position_restraint values?  That doesn't seem very elegant.

Thanks again for your help

Daniel


> Hi Daniel,
> 
> What you want is well possible. In the topology file for 
> the ligand (ligand.itp) add a something like:
> 
> [ position_restraint ]
>     1    1000    0    0
> 
> Here, the first number is an atom identifier, 
> corresponding to an atom under [ atoms ] and the number 
> are the force constants for the restraints in the x, y and 
> z direction. The directions in which it should move freely 
> should be set to 0, obviously. Also check the manual (in 
> case i misspelled something).
> 
> Hope it helps,
> 
> Tsjerk
> 
> 
> On 21 Apr 2005 17:37:37 +0000
>   Daniel Rigden <drigden at liverpool.ac.uk> wrote:
> > Hi all
> > 
> > Can anyone tell me if it's straightforward, or even 
> >possible to simulate
> > ligands that are attached to a surface?  The ligands are 
> >permanently
> > attached but may 'skate' around the two-dimensional 
> >surface.  I was
> > imagining that the atoms through which the ligands are 
> >attached could be
> > constrained in z while being free to explore x and y. 
> > All the other
> > atoms would explore x, y and z as normal.  Is that 
> >possible in Gromacs?
> > 
> > Thanks very much for any advice
> > 
> > Daniel
> > 
> > -- 
> > Dr Daniel John Rigden                     Tel:(+44) 151 
> >795 4467
> > School of Biological Sciences             FAX:(+44) 151 
> >795 4406
> > Room 101, Biosciences Building
> > University of Liverpool
> > Crown St.,
> > Liverpool L69 7ZB, U.K.
> > 
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> 
> 
> ------------------------------
> 
> Message: 9
> Date: Thu, 21 Apr 2005 21:37:56 +0200
> From: "T.A.Wassenaar" <T.A.Wassenaar at rug.nl>
> Subject: Re: [gmx-users] TUTORIAL FOR DRUG-ENZYME COMPLEX
> To: Vlad Scepanovsky <jaguar1 at ukr.net>,	Discussion list for GROMACS
> 	users <gmx-users at gromacs.org>
> Message-ID: <web-2854640 at mail3.rug.nl>
> Content-Type: text/plain; charset="windows-1251"; format="flowed"
> 
> 
> Hi Vlad,
> 
> I haven't heard of any tutorial for a covalently bound 
> drug enzyme complex. But getting the topology for the new 
> part is basically the same as in John's tutorial, and then 
> it's just stitching the topologies of the protein and the 
> new block together, defining (a) bonds(s), angle(s), 
> dihedrals, etc. (don't forget to think about additional 
> exclusions). If you have to do this several times over, it 
> may be worth defining a building block that can be 
> processed by pdb2gmx.
> And feel free to write a tutorial once you've managed.
> 
> Cheers,
> 
> Tsjerk
> 
> On Tue, 19 Apr 2005 11:49:45 +0300
>   "Vlad Scepanovsky" <jaguar1 at ukr.net> wrote:
> > 
> >  Dear David
> > Would you be so glad to tell me about any Tutorial for 
> >Drug-Enzyme Complex
> > but John E. Kerrigan's tutorial. The complex in named 
> >tutorial is NON-COVALENT, but
> > we need any information about COVALENT Drug-Enzyme 
> >Complexes.
> > 
> >                                                           
> >                Senserely yours
> >                                                           
> >                     Vladymyr Schepanovsky.
> >        
> >                               
> > _______________________________________________
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> > www interface or send it to 
> >gmx-users-request at gromacs.org.
> 
> 
> 
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> End of gmx-users Digest, Vol 12, Issue 35
> *****************************************
-- 
Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.