Re: [gmx-users] Monitoring of Salt bridges during simulation Run

[Mark Abraham]

 
 
On 05/04/12, James Starlight  wrote:

> Bharat, Peter thanks for advises
> 
> I've checked g_saltbr but not found possible definition of the specified 
> regions ( this utility lacks -n index.ndx option). How I could ignore 
> contacts between solvent and protein ?

 
Use trjconv -n and tpbconv -n to create a matching subset of your trajectory 
and -s input file, and use that as input to g_saltbr. 
 

> 
> 
> Also what is the real -t value should I provide ? As I understood this is 
> only Rmin but could I define Rmax cutoff as well?

 
Looks like Rmax to me, from g_saltbr -h, but if you experiment, find out and 
report back it can go into the next version of the documentation (which is 
never perfect!).
 
Mark 
 

> 
> 
> 
> James
> 
> 
> 5 апреля 2012 г. 12:36 пользователь Peter C. Lai  написал:
> 
> 
> > g_saltbr?
> > 
> > If you have salt bridges you already know about and want to look at, you
> > can always go with g_dist per pair manually.
> > 
> > 
> > On 2012-04-05 12:23:02PM +0400, James Starlight wrote:
> > > Dear Gromacs Users!
> > >
> > >
> > > I'd like to monitor origin and destabilisation of salt-bridges during
> > > simulation time. In particular I want to define some charged residues
> > > within selection groups to monitor both of intra-protein as well as
> > > protein-protein interactions. In past I've used only
> > 
> > > g_hbondutillity to
> > 
> > > monitor Hbonds within selection. Is there any specified program
> > > for such task but with salt-bridges only ?
> > >
> > >
> > > 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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> > 
> > 
> > --
> > 
> > ==
> > Peter C. Lai| University of Alabama-Birmingham
> > Programmer/Analyst  | KAUL 752A
> > Genetics, Div. of Research  | 705 South 20th Street
> > p...@uab.edu | Birmingham AL 35294-4461
> > (205) 690-0808  |
> > ==
> > 
> > 
> > 
> > --
> > 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] Monitoring of Salt bridges during simulation Run

[James Starlight]

Bharat, Peter thanks for advises

I've checked g_saltbr but not found possible definition of the specified
regions ( this utility lacks -n index.ndx option). How I could ignore
contacts between solvent and protein ?

Also what is the real *-t value should I provide ? As I understood this is
only Rmin but could I define Rmax cutoff as well?

James
*
5 апреля 2012 г. 12:36 пользователь Peter C. Lai  написал:

> g_saltbr?
>
> If you have salt bridges you already know about and want to look at, you
> can always go with g_dist per pair manually.
>
> On 2012-04-05 12:23:02PM +0400, James Starlight wrote:
> > Dear Gromacs Users!
> >
> >
> > I'd like to monitor origin and destabilisation of salt-bridges during
> > simulation time. In particular I want to define some charged residues
> > within selection groups to monitor both of intra-protein as well as
> > protein-protein interactions. In past I've used only
> > g_hbondutillity to
> > monitor Hbonds within selection. Is there any specified program
> > for such task but with salt-bridges only ?
> >
> >
> > 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!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> ==
> Peter C. Lai| University of Alabama-Birmingham
> Programmer/Analyst  | KAUL 752A
> Genetics, Div. of Research  | 705 South 20th Street
> p...@uab.edu | Birmingham AL 35294-4461
> (205) 690-0808  |
> ==
>
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Monitoring of Salt bridges during simulation Run

[Peter C. Lai]

g_saltbr?

If you have salt bridges you already know about and want to look at, you
can always go with g_dist per pair manually.

On 2012-04-05 12:23:02PM +0400, James Starlight wrote:
> Dear Gromacs Users!
> 
> 
> I'd like to monitor origin and destabilisation of salt-bridges during
> simulation time. In particular I want to define some charged residues
> within selection groups to monitor both of intra-protein as well as
> protein-protein interactions. In past I've used only
> g_hbondutillity to
> monitor Hbonds within selection. Is there any specified program
> for such task but with salt-bridges only ?
> 
> 
> 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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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Monitoring of Salt bridges during simulation Run

[bharat gupta]

You can use g_saltbr option , http://manual.gromacs.org/online/g_saltbr.html

On Thu, Apr 5, 2012 at 5:23 PM, James Starlight wrote:

> Dear Gromacs Users!
>
>
> I'd like to monitor origin and destabilisation of salt-bridges during
> simulation time. In particular I want to define some charged residues
> within selection groups to monitor both of intra-protein as well as
> protein-protein interactions. In past I've used only 
> g_hbondutillity to monitor 
> Hbonds within selection. Is there any specified program
> for such task but with salt-bridges only ?
>
>
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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South Korea
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Mobile no. - 010-5818-3680
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[gmx-users] Monitoring of Salt bridges during simulation Run

[James Starlight]

Dear Gromacs Users!


I'd like to monitor origin and destabilisation of salt-bridges during
simulation time. In particular I want to define some charged residues
within selection groups to monitor both of intra-protein as well as
protein-protein interactions. In past I've used only
g_hbondutillity to
monitor Hbonds within selection. Is there any specified program
for such task but with salt-bridges only ?


Thanks for help,

James
-- 
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