Re: [gmx-users] Making Disulfide Bonds

[Justin A. Lemkul]

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 in the .mdp file, 
hence why I pointed it out.  Complete information is always more effective.



*disre = simple

***disre_f = 5000



The latter is not a real keyword, but I'll assume you've done it right in the 
.mdp file.



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

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 ?



It doesn't seem like you've forgotten anything.  Depending on how far away the 
atoms are from one another in the starting structure, perhaps EM is simply not 
creating large enough structural changes to impose the desired geometry.  A 
distance restraint is simply a biasing potential, it is not a guarantee that 
certain geometry will be imposed, just made more likely.  Perhaps other aspects 
of the structure are preventing it from changing much.  Perhaps you need more EM 
steps, or maybe run a few steps of in vacuo MD to see if the structure adjusts.


-Justin

--


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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Re: [gmx-users] Making Disulfide Bonds

[James Starlight]

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

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 

>
>
> 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 > 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  10 10.18 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 >>
>>
>>
>>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 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
>>
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>Please search the archive at
>>
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>> > >.
>>
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>>
>>
>>
>>
>>--
>>Cordiali saluti, Dr.Oteri Francesco
>>
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Re: [gmx-users] Making Disulfide Bonds

[Justin A. Lemkul]

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 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  10 10.18 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 mailto: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 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


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Re: [gmx-users] Making Disulfide Bonds

[Francesco Oteri]

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 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.




2012/4/28 James Starlight >


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. Does it correct ? Or should I use 
some other disres for such task ?

James



2012/4/28 francesco oteri mailto: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 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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Re: [gmx-users] Making Disulfide Bonds

[James Starlight]

.. 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.



2012/4/28 James Starlight 

> 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. Does it correct ? Or should I use some 
> other disres for such task ?
>
> James
>
>
>
> 2012/4/28 francesco oteri 
>
>> 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 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
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> Cordiali saluti, Dr.Oteri Francesco
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
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Re: [gmx-users] Making Disulfide Bonds

[James Starlight]

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. Does it correct ? Or should I
use some other disres for such task ?

James



2012/4/28 francesco oteri 

> 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 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
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
> --
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Re: [gmx-users] Making Disulfide Bonds

[francesco oteri]

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 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
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
Cordiali saluti, Dr.Oteri Francesco
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