[gmx-users] ligands bound to a surface

[T.A.Wassenaar]

Hi Daniel,

You could do that, but indeed it's not very elegant. 
Rather, make the surface a freeze group. That way it won't 
do anything itself, except being present and keeping other 
molecules from going that way.

Cheers,

Tsjerk


On 22 Apr 2005 11:02:59 +0000
  Daniel Rigden <drigden at liverpool.ac.uk> wrote:
> 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.
>> > 
>> > _______________________________________________
>> > gmx-users mailing list
>> > gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please don't post (un)subscribe requests to the list. 
>> >Use the 
>> > www interface or send it to 
>> >gmx-users-request at gromacs.org.
>> 
>> 
>> 
>> ------------------------------
>> 
>> 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.
>> >        
>> >                               
>> > _______________________________________________
>> > gmx-users mailing list
>> > gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please don't post (un)subscribe requests to the list. 
>> >Use the 
>> > www interface or send it to 
>> >gmx-users-request at gromacs.org.
>> 
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> 
>> 
>> 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.
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. 
>Use the 
> www interface or send it to 
>gmx-users-request at gromacs.org.