On 4/28/12 10:08 AM, James Starlight wrote:
.. and the main question- what should be in mdp file of such restrained
minimisation ?
Today I've done vry properly minimisation of such system in vacuum with the CG
minimisator and applied disres ( above example ) with big force constant (
disres options have been defined in the minim.mdp file ). As the result I have
not noticed any perturbation in the distance between two S-S atoms the distance
between wich I've constrained.
You need to add the applicable distance restraint settings for them to be
utilized.
http://manual.gromacs.org/online/mdp_opt.html#nmr
-Justin
2012/4/28 James Starlight <[email protected]
<mailto:[email protected]>>
Hi Francesco!
So I must define in the current topology the disres bettwen two S atoms ( in
the below example 1 and 10 ) to apply hormonic restains
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1 10 1 0 1 0.18 0.20 0.22 1.0
to restrain this atoms within 0.2 nm. Does it correct ? Or should I use
some other disres for such task ?
James
2012/4/28 francesco oteri <[email protected]
<mailto:[email protected]>>
Hi James,
usually people run a minimization using distance restrain on the two
atoms in order to
make them closer.
Then the obtained cnfiguration is used to recalculate the topology.
Francesco
2012/4/28 James Starlight <[email protected]
<mailto:[email protected]>>
Dear Gromacs Users!
I have a model of my protein wich has 4 S-S bounds in the loop
regions. So I want to define in topology all those four S-S linkage.
Unfortunatelly one of that S-S have not been recognised by Gromacs (
Also I've tried to check this bond in pymol and found that distance
between that two Cys Cys are larger for S-S occurence) due to some
inaccyracy of model.
Is there any way to define such missing S-S manually? On the gromacs
site I've found possible sollution by means of spechbond.dat
editing. I've tried to increase distance between S-S atoms but this
have not had desirebly affect.
In the topology.top file I've found that the S-S bonds beetween S
atoms are defined in the bond section without any type for such bond
type. Also I've found that the same enties are present in the angle
and dihedralls sections. Could I define the same contact only in
the bond section and further minimise my system to obtain new S-S
linckage or should I also define all other enties ( like dihedralls
etc) for that bond ?
Thanks for help
James
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Cordiali saluti, Dr.Oteri Francesco
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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