[gmx-users] Generation of the Distance Restraints

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 28 22:58:56 CEST 2012

On 29/03/2012 5:53 AM, James Starlight wrote:
> Mark,
> thanks for explanation again.
> 28 ????? 2012 ?. 16:04 ???????????? Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> ???????:
>      That can mean big restraint forces and tiny integration steps and
>     lots of tweaking and praying.
> Yes I think this aproach could be usefull in my case. Actually I want 
> to move some parts of the helices of my protein in the deired 
> direction up to 6-10 A. There is the data showing that this new 
> conformation is very unstabile and short-lived in the absense of some 
> additional external factors. But also I've seen that application of 
> big restrained forces perturbed the overal structure of my protein 
> considerably. So the good sollution might be application of such 
> forces  with the position restraines simultaneously. What do you think 
> about the most trivial aproach: e.g if I could not applied posres on 
> the desired atoms and use default posres generated by pdb2gmx on the 
> all atoms. At the same time I'm using more strongest distance 
> restrains on the desired positions to move this atoms even the 
> precense of weaker posres applied on this. Finally because posres act 
> on the others atoms I can prevent destabilisation of the whole 
> protein. Might this aproach be usefull? And what difference between 
> forses of the posres ( 1000 kj) and disres must be to generate 
> expected effect ?

Yeah, some kind of hybrid treatment of distance and position restraints 
could be required. I've no idea on required force constants - this kind 
of thing (breaking the force field to set up initial conditions that you 
expect are fairly unphysical) is very situation dependent. Nobody really 
does it often enough for there to be a general body of knowledge.

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