Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Thankyou!

On Fri, Jan 10, 2020 at 6:00 AM Justin Lemkul  wrote:

>
>
> On 1/9/20 9:42 AM, Navneet Kumar wrote:
> > Thank You, sir!
> >
> > What If I want to extend the residues like choose c-alpha of 150-200 &
> > 60-70 in a single index group ?
>
> 3 & r 60-70 | 3 & r 150-200
>
> Type "help" at the make_ndx prompt for examples of how to use the program.
>
> -Justin
>
> >
> > On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul  wrote:
> >
> >>
> >> On 1/8/20 4:49 AM, Christian Blau wrote:
> >>> Hi Navnett,
> >>>
> >>>
> >>> gmx select will be your friend.
> >>>
> >>>
> >>> At the bottom of
> >>>
> >>>
> >>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
> >>>
> >>> you'll find some example commands. Something along the lines of
> >>>
> >>>gmx select -select 'name CA and resid > 149 and resid < 211'
> >>>
> >>> should work.
> >>>
> >>>
> >>> It's a very powerful syntax and I figured for me it was very much
> >>> worth the effort reading through that documentation.
> >>>
> >> It's also simple in make_ndx:
> >>
> >> 3 & r 150-210
> >>
> >> Either way works. Whatever you find easier to use.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Justin Lemkul]

On 1/9/20 9:42 AM, Navneet Kumar wrote:

Thank You, sir!

What If I want to extend the residues like choose c-alpha of 150-200 &
60-70 in a single index group ?


3 & r 60-70 | 3 & r 150-200

Type "help" at the make_ndx prompt for examples of how to use the program.

-Justin



On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul  wrote:



On 1/8/20 4:49 AM, Christian Blau wrote:

Hi Navnett,


gmx select will be your friend.


At the bottom of



http://manual.gromacs.org/documentation/current/onlinehelp/selections.html


you'll find some example commands. Something along the lines of

   gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much
worth the effort reading through that documentation.


It's also simple in make_ndx:

3 & r 150-210

Either way works. Whatever you find easier to use.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Thank You, sir!

What If I want to extend the residues like choose c-alpha of 150-200 &
60-70 in a single index group ?


On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul  wrote:

>
>
> On 1/8/20 4:49 AM, Christian Blau wrote:
> > Hi Navnett,
> >
> >
> > gmx select will be your friend.
> >
> >
> > At the bottom of
> >
> >
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
> >
> >
> > you'll find some example commands. Something along the lines of
> >
> >   gmx select -select 'name CA and resid > 149 and resid < 211'
> >
> > should work.
> >
> >
> > It's a very powerful syntax and I figured for me it was very much
> > worth the effort reading through that documentation.
> >
>
> It's also simple in make_ndx:
>
> 3 & r 150-210
>
> Either way works. Whatever you find easier to use.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.



-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Justin Lemkul]

On 1/8/20 4:49 AM, Christian Blau wrote:

Hi Navnett,


gmx select will be your friend.


At the bottom of

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html 



you'll find some example commands. Something along the lines of

  gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much 
worth the effort reading through that documentation.




It's also simple in make_ndx:

3 & r 150-210

Either way works. Whatever you find easier to use.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Thank You, Sir!

On Wed, Jan 8, 2020 at 3:19 PM Christian Blau  wrote:

> Hi Navnett,
>
>
> gmx select will be your friend.
>
>
> At the bottom of
>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
>
> you'll find some example commands. Something along the lines of
>
>gmx select -select 'name CA and resid > 149 and resid < 211'
>
> should work.
>
>
> It's a very powerful syntax and I figured for me it was very much worth
> the effort reading through that documentation.
>
>
> Best,
>
> Chrsitian
>
> On 2020-01-08 10:42, Navneet Kumar wrote:
> > Sorry, it should be 150-200 residues.
> >
> > On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar 
> wrote:
> >
> >> Hello Everyone!
> >>
> >>
> >> How to create an index group for Backbone/C-alpha for a specific set of
> >> residues from protein? (Say Protein with 200 amino acid; want to create
> an
> >> index group for the backbone of residues 150-210).
> >> Regards
> >> Navneet Kumar
> >>
> >>
> >>
> >>
> >>
> >>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.



-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Christian Blau]

Hi Navnett,


gmx select will be your friend.


At the bottom of

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html

you'll find some example commands. Something along the lines of

  gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much worth the 
effort reading through that documentation.


Best,

Chrsitian

On 2020-01-08 10:42, Navneet Kumar wrote:

Sorry, it should be 150-200 residues.

On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar  wrote:


Hello Everyone!


How to create an index group for Backbone/C-alpha for a specific set of
residues from protein? (Say Protein with 200 amino acid; want to create an
index group for the backbone of residues 150-210).
Regards
Navneet Kumar







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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Sorry, it should be 150-200 residues.

On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar  wrote:

> Hello Everyone!
>
>
> How to create an index group for Backbone/C-alpha for a specific set of
> residues from protein? (Say Protein with 200 amino acid; want to create an
> index group for the backbone of residues 150-210).
> Regards
> Navneet Kumar
>
>
>
>
>
>

-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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* Please search the archive at 
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