On 29/03/2012 5:53 AM, James Starlight wrote:
Mark,
thanks for explanation again.
28 ????? 2012 ?. 16:04 ???????????? Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@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.
Mark
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