Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread Syma Khalid 
Hi,

If the position restraints are only on the protein, then the water and lipids 
are free to move about- assuming you have a cavity in your protein wide enough 
to accommodate water- then water (or lipids) depending on the nature and 
location of the cavity, should move in as a vacuum is not energetically 
favored. 

If you wish to place waters in the pore/cavity yourself prior to simulation, 
there are codes available that can do this (vmd has a plugin i think), you can 
also use voidoo and flood. I have never used to gromacs to do this- but it is 
likely someone else has, did you check the archives?

Best wishes,

-Syma


In message <[EMAIL PROTECTED]> minnale  <[EMAIL PROTECTED]>, Discussion list 
for GROMACS users  writes:
>   Thanks for your prompt reply, according to you for membrane protein 
> protocols keep restrain only on protein but not on lipid and water, is there 
> any possibility to move water inside pore of the membrane when keep restrain 
> only on protein.
> Could you please tell me
> Thanks a lot in advance 
> 
> 
> On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
> >
> >
> >minnale wrote:
> >>
> >>  HI users,
> >>   I have embedded protein in popc bilayer and ran the minimisation 
> >> succesfully , before going equilibration I would like to confirm one thing 
> >> that how to run the equilibration with on which system keep position 
> >> restrain?
> >>
> >>1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
> >>-DPOSRES_LIPID, -DPOSRES_WATER) at a time ?
> >>
> >>or 2. keep position resrain on each system at a time and
> >>   3.is it require to keep position restrain on water?
> >>Could you tell me clearly pls
> >>Thanks alot in advance
> >>
> >>
> >
> >If you "equilibrate" your system with every element of it restrained, I 
> >think you will accomplish absolutely nothing.  Typical procedures for 
> >membrane proteins involve equilibrating with restraints on the protein only, 
> >allowing the lipids to pack around the protein. 
> >-Justin
> >
> >>
> >>HSBC 
> >> >> PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> 
> >>
> >>
> >>
> >>___
> >>gmx-users mailing listgmx-users@gromacs.org
> >>http://www.gromacs.org/mailman/listinfo/gmx-users
> >>Please search the archive at http://www.gromacs.org/search before posting!
> >>Please don't post (un)subscribe requests to the list. Use the www interface 
> >>or send it to [EMAIL PROTECTED]
> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >-- 
> >
> >Justin A. Lemkul
> >Graduate Research Assistant
> >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: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread minnale 
  Thanks for your invaluable reply to Justin and syma.


On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>
>>   Thanks for your prompt reply, according to you for membrane protein 
>> protocols keep restrain only on protein but not on lipid and water, is there 
>> any possibility to move water inside pore of the membrane when keep restrain 
>> only on protein.
>>Could you please tell me
>>Thanks a lot in advance
>>
>
>Anything is possible, given the random nature of MD.  It will depend largely 
>upon how you prepared your system.  If there is a lot of void space around 
>your protein, then water will likely leak in over time, but may be forced out 
>by the hydrophobic lipid tails, if you equilibrate long enough.  If your 
>lipids are nicely packed around your protein (using a method like InflateGRO 
>from Tieleman's site) then this occurrence is less likely.
>
>The most important thing to do is to consult the literature regarding similar 
>systems and take note of what those authors have done.  How did they insert 
>the protein?  How did they equilibrate the system, and for how long?
>
>-Justin
>
>>
>>On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
>> >
>> >
>> >minnale wrote:
>> >>
>> >>  HI users,
>> >>  I have embedded protein in popc bilayer and ran the minimisation 
>> >> succesfully , before going equilibration I would like to confirm one 
>> >> thing that how to run the equilibration with on which system keep 
>> >> position restrain?
>> >>
>> >>1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
>> >>-DPOSRES_LIPID, -DPOSRES_WATER) at a time ?
>> >>
>> >>or 2. keep position resrain on each system at a time and
>> >>  3.is it require to keep position restrain on water?
>> >>Could you tell me clearly pls
>> >>Thanks alot in advance
>> >>
>> >>
>> >
>> >If you "equilibrate" your system with every element of it restrained, I 
>> >think you will accomplish absolutely nothing.  Typical procedures for 
>> >membrane proteins involve equilibrating with restraints on the protein 
>> >only, allowing the lipids to pack around the protein.
>> >-Justin
>> >
>> >>
>> >>HSBC 
>> >>> >> PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> 
>> >>
>> >>
>> >>
>> >>___
>> >>gmx-users mailing listgmx-users@gromacs.org
>> >>http://www.gromacs.org/mailman/listinfo/gmx-users
>> >>Please search the archive at http://www.gromacs.org/search before posting!
>> >>Please don't post (un)subscribe requests to the list. Use the www 
>> >>interface or send it to [EMAIL PROTECTED]
>> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> >-- 
>> >
>> >Justin A. Lemkul
>> >Graduate Research Assistant
>> >Department of Biochemistry
>> >Virginia Tech
>> >Blacksburg, VA
>> >jalemkul[at]vt.edu | (540) 231-9080
>> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> >
>> >
>>
>>
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www interface 
>>or send it to [EMAIL PROTECTED]
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>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] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread Justin A. Lemkul 



minnale wrote:


  Thanks for your prompt reply, according to you for membrane protein 
protocols keep restrain only on protein but not on lipid and water, is 
there any possibility to move water inside pore of the membrane when 
keep restrain only on protein.

Could you please tell me
Thanks a lot in advance



Anything is possible, given the random nature of MD.  It will depend 
largely upon how you prepared your system.  If there is a lot of void 
space around your protein, then water will likely leak in over time, but 
may be forced out by the hydrophobic lipid tails, if you equilibrate 
long enough.  If your lipids are nicely packed around your protein 
(using a method like InflateGRO from Tieleman's site) then this 
occurrence is less likely.


The most important thing to do is to consult the literature regarding 
similar systems and take note of what those authors have done.  How did 
they insert the protein?  How did they equilibrate the system, and for 
how long?


-Justin



On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>
>>  HI users,
>>  I have embedded protein in popc bilayer and ran the 
minimisation succesfully , before going equilibration I would like to 
confirm one thing that how to run the equilibration with on which 
system keep position restrain?

>>
>>1.we will keep position restrain on all the 
systems(-DPOSRES_PROTEIN, -DPOSRES_LIPID, -DPOSRES_WATER) at a time ?

>>
>>or 2. keep position resrain on each system at a time and
>>  3.is it require to keep position restrain on water?
>>Could you tell me clearly pls
>>Thanks alot in advance
>>
>>
>
>If you "equilibrate" your system with every element of it restrained, 
I think you will accomplish absolutely nothing.  Typical procedures 
for membrane proteins involve equilibrating with restraints on the 
protein only, allowing the lipids to pack around the protein.

>-Justin
>
>>
>>HSBC 
 


>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before 
posting!
>>Please don't post (un)subscribe requests to the list. Use the www 
interface or send it to [EMAIL PROTECTED]

>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>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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--


Justin A. Lemkul
Graduate Research Assistant
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: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread minnale 
  Thanks for your prompt reply, according to you for membrane protein protocols 
keep restrain only on protein but not on lipid and water, is there any 
possibility to move water inside pore of the membrane when keep restrain only 
on protein.
Could you please tell me
Thanks a lot in advance 


On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>
>>  HI users,
>>   I have embedded protein in popc bilayer and ran the minimisation 
>> succesfully , before going equilibration I would like to confirm one thing 
>> that how to run the equilibration with on which system keep position 
>> restrain?
>>
>>1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
>>-DPOSRES_LIPID, -DPOSRES_WATER) at a time ?
>>
>>or 2. keep position resrain on each system at a time and
>>   3.is it require to keep position restrain on water?
>>Could you tell me clearly pls
>>Thanks alot in advance
>>
>>
>
>If you "equilibrate" your system with every element of it restrained, I think 
>you will accomplish absolutely nothing.  Typical procedures for membrane 
>proteins involve equilibrating with restraints on the protein only, allowing 
>the lipids to pack around the protein. 
>-Justin
>
>>
>>HSBC 
>>> PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> 
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www interface 
>>or send it to [EMAIL PROTECTED]
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>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: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread minnale 
  Thanks for your prompt reply, according to you for membrane protein protocols 
keep restrain only on protein but not on lipid and water, is there any 
possibility to move water inside pore of the membrane when keep restrain only 
on protein.
Could you please tell me
Thanks a lot in advance 


On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>
>>  HI users,
>>   I have embedded protein in popc bilayer and ran the minimisation 
>> succesfully , before going equilibration I would like to confirm one thing 
>> that how to run the equilibration with on which system keep position 
>> restrain?
>>
>>1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
>>-DPOSRES_LIPID, -DPOSRES_WATER) at a time ?
>>
>>or 2. keep position resrain on each system at a time and
>>   3.is it require to keep position restrain on water?
>>Could you tell me clearly pls
>>Thanks alot in advance
>>
>>
>
>If you "equilibrate" your system with every element of it restrained, I think 
>you will accomplish absolutely nothing.  Typical procedures for membrane 
>proteins involve equilibrating with restraints on the protein only, allowing 
>the lipids to pack around the protein. 
>-Justin
>
>>
>>HSBC 
>>> PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> 
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www interface 
>>or send it to [EMAIL PROTECTED]
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>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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[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread minnale 
  
HI users,
   I have embedded protein in popc bilayer and ran the minimisation 
succesfully , before going equilibration I would like to confirm one thing that 
how to run the equilibration with on which system keep position restrain?

1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
-DPOSRES_LIPID, -DPOSRES_WATER) at a time ? 

or 2. keep position resrain on each system at a time and
   3.is it require to keep position restrain on water?
Could you tell me clearly pls
Thanks alot in advance___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread Justin A. Lemkul 



minnale wrote:


 
HI users,
  I have embedded protein in popc bilayer and ran the minimisation 
succesfully , before going equilibration I would like to confirm one 
thing that how to run the equilibration with on which system keep 
position restrain?


1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
-DPOSRES_LIPID, -DPOSRES_WATER) at a time ?


or 2. keep position resrain on each system at a time and
  3.is it require to keep position restrain on water?
Could you tell me clearly pls
Thanks alot in advance




If you "equilibrate" your system with every element of it restrained, I 
think you will accomplish absolutely nothing.  Typical procedures for 
membrane proteins involve equilibrating with restraints on the protein 
only, allowing the lipids to pack around the protein. 


-Justin



HSBC 
 





___
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--


Justin A. Lemkul
Graduate Research Assistant
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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[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

2008-06-29 Thread minnale 
  
HI users,
   I have embedded protein in popc bilayer and ran the minimisation 
succesfully , before going equilibration I would like to confirm one thing that 
how to run the equilibration with on which system keep position restrain?

1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, 
-DPOSRES_LIPID, -DPOSRES_WATER) at a time ? 

or 2. keep position resrain on each system at a time and
   3.is it require to keep position restrain on water?
Could you tell me clearly pls
Thanks alot in advance___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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