Re: [gmx-users] error in index file

2018-04-03 Thread Justin Lemkul 



On 4/3/18 5:50 AM, Joe Jordan wrote:

Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018
and using gmx select. Short of that, if you just run make_ndx and don't use
a selection sting you will get a group corresponding to NAP with the right
number of atoms.


Neither gmx select nor gmx make_ndx should be necessary here. All 
defined [moleculetypes] are default index groups. The ligand should show 
up as a choice from any GROMACS program without needing an index file at 
all.


-Justin


On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal 
wrote:


I'm using v4.6.2

$make_ndx -f npt.gro


r 306 (residue num of ligand)
name 24 Ligand

This should do the work right ?

On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan  wrote:


I got a group with the right number of atoms when I tried it. What

version

of gromacs are you using and what selection string are you using?

On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
wrote:


Location of the files:
https://drive.google.com/drive/u/0/folders/0B6O-
L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU

On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan 

wrote:

Can you post the gro file and the resulting index file?

On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <

abhisek.m...@gmail.com>

wrote:


Hi,

I'm just having some issue creating index file for umbrella

sampling.

I have a ligand:
Group20 (NAP) has73 elements

Now when I run following command:
gmx make_ndx -f npt.gro

and try to add NAP for index.ndx, only 6 elements were being added.

I don't understand the problem here.

NAP is clearly showing is of 73 elements, but how come it is

showing

me 6

elements when added to index file ?

Please help me out here.

Thanks.

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
--
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--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
--
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] error in index file

2018-04-03 Thread Joe Jordan 
Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018
and using gmx select. Short of that, if you just run make_ndx and don't use
a selection sting you will get a group corresponding to NAP with the right
number of atoms.

On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal 
wrote:

> I'm using v4.6.2
>
> $make_ndx -f npt.gro
>
> > r 306 (residue num of ligand)
> > name 24 Ligand
>
> This should do the work right ?
>
> On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan  wrote:
>
> > I got a group with the right number of atoms when I tried it. What
> version
> > of gromacs are you using and what selection string are you using?
> >
> > On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
> > wrote:
> >
> > > Location of the files:
> > > https://drive.google.com/drive/u/0/folders/0B6O-
> > > L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
> > >
> > > On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan 
> > wrote:
> > >
> > > > Can you post the gro file and the resulting index file?
> > > >
> > > > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <
> > abhisek.m...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I'm just having some issue creating index file for umbrella
> sampling.
> > > > >
> > > > > I have a ligand:
> > > > > Group20 (NAP) has73 elements
> > > > >
> > > > > Now when I run following command:
> > > > > gmx make_ndx -f npt.gro
> > > > >
> > > > > and try to add NAP for index.ndx, only 6 elements were being added.
> > > > >
> > > > > I don't understand the problem here.
> > > > >
> > > > > NAP is clearly showing is of 73 elements, but how come it is
> showing
> > > me 6
> > > > > elements when added to index file ?
> > > > >
> > > > > Please help me out here.
> > > > >
> > > > > Thanks.
> > > > >
> > > > > --
> > > > > Abhisek Mondal
> > > > >
> > > > > *Senior Research Fellow*
> > > > >
> > > > > *Structural Biology and Bioinformatics Division*
> > > > > *CSIR-Indian Institute of Chemical Biology*
> > > > >
> > > > > *Kolkata 700032*
> > > > >
> > > > > *INDIA*
> > > > > --
> > > > > 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.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Joe Jordan
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
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> > > >
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
> > > 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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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Joe Jordan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>



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Re: [gmx-users] error in index file

2018-04-03 Thread abhisek Mondal 
I'm using v4.6.2

$make_ndx -f npt.gro

> r 306 (residue num of ligand)
> name 24 Ligand

This should do the work right ?

On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan  wrote:

> I got a group with the right number of atoms when I tried it. What version
> of gromacs are you using and what selection string are you using?
>
> On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
> wrote:
>
> > Location of the files:
> > https://drive.google.com/drive/u/0/folders/0B6O-
> > L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
> >
> > On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan 
> wrote:
> >
> > > Can you post the gro file and the resulting index file?
> > >
> > > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <
> abhisek.m...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I'm just having some issue creating index file for umbrella sampling.
> > > >
> > > > I have a ligand:
> > > > Group20 (NAP) has73 elements
> > > >
> > > > Now when I run following command:
> > > > gmx make_ndx -f npt.gro
> > > >
> > > > and try to add NAP for index.ndx, only 6 elements were being added.
> > > >
> > > > I don't understand the problem here.
> > > >
> > > > NAP is clearly showing is of 73 elements, but how come it is showing
> > me 6
> > > > elements when added to index file ?
> > > >
> > > > Please help me out here.
> > > >
> > > > Thanks.
> > > >
> > > > --
> > > > Abhisek Mondal
> > > >
> > > > *Senior Research Fellow*
> > > >
> > > > *Structural Biology and Bioinformatics Division*
> > > > *CSIR-Indian Institute of Chemical Biology*
> > > >
> > > > *Kolkata 700032*
> > > >
> > > > *INDIA*
> > > > --
> > > > 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.
> > > >
> > >
> > >
> > >
> > > --
> > > Joe Jordan
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Joe Jordan
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
Gromacs Users mailing list

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

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Re: [gmx-users] error in index file

2018-04-03 Thread Joe Jordan 
I got a group with the right number of atoms when I tried it. What version
of gromacs are you using and what selection string are you using?

On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal 
wrote:

> Location of the files:
> https://drive.google.com/drive/u/0/folders/0B6O-
> L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
>
> On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan  wrote:
>
> > Can you post the gro file and the resulting index file?
> >
> > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal 
> > wrote:
> >
> > > Hi,
> > >
> > > I'm just having some issue creating index file for umbrella sampling.
> > >
> > > I have a ligand:
> > > Group20 (NAP) has73 elements
> > >
> > > Now when I run following command:
> > > gmx make_ndx -f npt.gro
> > >
> > > and try to add NAP for index.ndx, only 6 elements were being added.
> > >
> > > I don't understand the problem here.
> > >
> > > NAP is clearly showing is of 73 elements, but how come it is showing
> me 6
> > > elements when added to index file ?
> > >
> > > Please help me out here.
> > >
> > > Thanks.
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > Joe Jordan
> > --
> > 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.
> >
>
>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> 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.
>



-- 
Joe Jordan
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Re: [gmx-users] error in index file

2018-04-03 Thread abhisek Mondal 
Location of the files:
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU

On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan  wrote:

> Can you post the gro file and the resulting index file?
>
> On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal 
> wrote:
>
> > Hi,
> >
> > I'm just having some issue creating index file for umbrella sampling.
> >
> > I have a ligand:
> > Group20 (NAP) has73 elements
> >
> > Now when I run following command:
> > gmx make_ndx -f npt.gro
> >
> > and try to add NAP for index.ndx, only 6 elements were being added.
> >
> > I don't understand the problem here.
> >
> > NAP is clearly showing is of 73 elements, but how come it is showing me 6
> > elements when added to index file ?
> >
> > Please help me out here.
> >
> > Thanks.
> >
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > 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.
> >
>
>
>
> --
> Joe Jordan
> --
> 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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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
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] error in index file

2018-04-03 Thread Joe Jordan 
Can you post the gro file and the resulting index file?

On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal 
wrote:

> Hi,
>
> I'm just having some issue creating index file for umbrella sampling.
>
> I have a ligand:
> Group20 (NAP) has73 elements
>
> Now when I run following command:
> gmx make_ndx -f npt.gro
>
> and try to add NAP for index.ndx, only 6 elements were being added.
>
> I don't understand the problem here.
>
> NAP is clearly showing is of 73 elements, but how come it is showing me 6
> elements when added to index file ?
>
> Please help me out here.
>
> Thanks.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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[gmx-users] error in index file

2018-04-03 Thread abhisek Mondal 
Hi,

I'm just having some issue creating index file for umbrella sampling.

I have a ligand:
Group20 (NAP) has73 elements

Now when I run following command:
gmx make_ndx -f npt.gro

and try to add NAP for index.ndx, only 6 elements were being added.

I don't understand the problem here.

NAP is clearly showing is of 73 elements, but how come it is showing me 6
elements when added to index file ?

Please help me out here.

Thanks.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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