[gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Wed Mar 28 20:53:28 CEST 2012


thanks for explanation again.

28 марта 2012 г. 16:04 пользователь Mark Abraham
<Mark.Abraham at anu.edu.au>написал:

 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 ?


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