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 1 0 1 0.18 0.20 0.22 1.0
where 1 and 10 the numbers of the S atoms of both Cys residues. and 0.2 is
the disered distance between wich I want to obtain after such minimisation.
*
As the consequence no changes have been detected after such CG minimisation
:( What I've forgotten ?
James
*
2012/4/28 Justin A. Lemkul <jalem...@vt.edu>
>
>
> 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<http://manual.gromacs.org/online/mdp_opt.html#nmr>
>
> -Justin
>
>
>>
>> 2012/4/28 James Starlight <jmsstarli...@gmail.com <mailto:
>> jmsstarli...@gmail.com**>>
>>
>>
>> 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 <francesco.ot...@gmail.com
>> <mailto:francesco.oteri@gmail.**com <francesco.ot...@gmail.com>>>
>>
>>
>> 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 <jmsstarli...@gmail.com
>> <mailto:jmsstarli...@gmail.com**>>
>>
>>
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
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