[gmx-users] Tethering

[Joanne Hanna]

Hi

Thank you, I had misunderstood what the purpose of the position restraints file. If I have a protein posre.itp and ligand posre.ipt files do i leave them all as seperate files of the same name or do I combine then, also where do i define the force constant and if i have had to make a topology file (which I have had to for an AMP ligand) how do i generate a position restraints file for this?

Many thanks
Jo

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk
jfhanna at gmail.com
>>> T.A.Wassenaar at rug.nl 05/06/05 15:44 PM >>>

Hi Joanne,

What you want are position_restraints, applied to protein 
atoms (incl. ligand) and with a relatively low force 
constant (200).

Check the manual on position restrained md, or check any 
gromacs tutorial.

Cheers,

Tsjerk

On Fri, 06 May 2005 15:29:20 +0100
  "Joanne Hanna" <J.F.Hanna at warwick.ac.uk> wrote:
> I am probably going to show my ignorance now but want i 
>want to do is allow the protein to move slightly but 
>always back to the same place, so as to remove any 
>unfavourable waters.
> 
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
> 
> J.F.Hanna at warwick.ac.uk
> jfhanna at gmail.com
>>>> spoel at xray.bmc.uu.se 05/06/05 15:22 PM >>>
> On Fri, 6 May 2005, Joanne Hanna wrote:
> 
>>Hi
>>
>>could anybody please tell me a way to tether my protein, 
>>rather than freeze it. I want to run an MD simulation 
>>with my enzyme and ligands tethered whilst allowing the 
>>solvent to move freely.
>>
> do you mean with position restraints?
> 
>>Thanks
>>Jo
>>
>>Joanne Hanna
>>Department of Chemistry
>>University of Warwick
>>Coventry
>>CV4 7AL
>>
>>J.F.Hanna at warwick.ac.uk
>>jfhanna at gmail.com
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> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular 
>Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org 
>  http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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