On 4/28/12 10:25 AM, James Starlight wrote:
Francesco,
Thanks, I find your aproach very handfull :)
Justin,
in that example I've defined in minim.mdp
This would have been useful to state up front. Your previous question implied
that you didn't know if any special keywords were necessary
Francesco,
Thanks, I find your aproach very handfull :)
Justin,
in that example I've defined in minim.mdp
*disre = simple
**disre_f = 5000
in the topology.top I've included
* [ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1 10 10 10.18 0.20 0.22 1.0
w
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 op
Hi James,
usually I insert by hand a bond in the topology file between the two
atoms and then I minimize.
This bond doesn't cause the generataion of angles and dihedrals, butit
is enough to make the atom closer.
Francesco
Il 28/04/2012 16:08, James Starlight ha scritto:
.. and the main questi
.. 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 ).
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 10 10.18 0.20 0.22 1.0
to restrain this atoms within 0.2 nm. Doe
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
> Dear Gromacs Users!
>
> I have a model of my protein wich has 4 S-S bounds
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
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