[gmx-users] Tethering

[David van der Spoel]

On Fri, 6 May 2005, Joanne Hanna wrote:

>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?
there is a utility called genpr

>
>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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-- 
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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