Re: [gmx-users] Plot renumbering

2010-01-29 Thread Justin A. Lemkul 



rituraj purohit wrote:

Hello friends,

As Justin replied at carla query about structure deformation after the 
pdb2gmx & the new number retain till end.


My PDB starts at 24 to 200 aa, While running xmgrace (after complete 
simulation) the rmsd plot is from 1 to 176aa.


I understood by previous mail that gromacs renumbered my pdb file at 
first step.
My question is, Is their any way to get plot from 24 to 200 (as entry in 
pdb) rather 1 to 174 ?


Write a script that renumbers the file - perl, awk, sed, etc.  I think pdb2gmx 
renumbering is being removed in the development code for future versions, FYI.


-Justin



Regard
Rituraj

On Fri, Jan 29, 2010 at 7:28 PM, > wrote:


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Today's Topics:

  1. Re: Structure deformation (Carla Jamous)
  2. Re: Structure deformation (Justin A. Lemkul)
  3. Re: Re: including a custom itp file in topology (Tsjerk Wassenaar)
  4. Re: RE: xmgrace (bharat gupta)
  5. Re: RE: xmgrace (Justin A. Lemkul)
  6. Re: RE: xmgrace (Baofu Qiao)


--

Message: 1
Date: Fri, 29 Jan 2010 14:03:12 +0100
From: Carla Jamous mailto:carlajam...@gmail.com>>
Subject: Re: [gmx-users] Structure deformation
To: jalem...@vt.edu , Discussion list for
GROMACS users
   mailto:gmx-users@gromacs.org>>
Message-ID:
   mailto:e02c90f11001290503yce52eb7w45f7f23a53250...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

Thank you Justin,
you were right I was looking at the wrong residue numbers.

I have another question that may also sound stupid, but I can't
figure it
out:
I want to extract from my trajectory, the protein, the ligand and ions.
However, when I try to do that with trjconv -f .trr -s .trr -n .ndx
gromacs asks to choose a group from my index file.
But if I choose group 0 1 2
it only takes the first group without the rest.
So how can I extract many groups at once from my trajectory?

Carla

On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:

 >
 >
 > Carla Jamous wrote:
 >
 >> Hi everyone,
 >> I have a question about structure deformation
 >> Can pdb2gmx alter secondary structures of my protein, while adding
 >> hydrogens. Because I had a helix in my protein, that became a
beta-sheet
 >> after pdb2gmx.
 >>
 >
 > Sorry to say, but this sounds completely unlikely.  A bug of this
magnitude
 > surely would've been noticed long ago.
 >
 >
 >  What may be the problem?
 >>
 >>
 > Are you certain you're looking at the same residues?  pdb2gmx
renumbers
 > from 1, so if there are missing N-terminal residues, they will
not have the
 > same numbers  before and after pdb2gmx.
 >
 > -Justin
 >
 >  Thank you
 >> Carla
 >>
 >>
 > --
 > 
 >
 > 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
 >
 > 
 > --
 > gmx-users mailing listgmx-users@gromacs.org

 > http://lists.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 gmx-users-requ...@gromacs.org
.
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >
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Message: 2
Date: Fri, 29 Jan 2010 08:04:11 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Structure deformation
To: "Gromacs Users' List" mailt

[gmx-users] Plot renumbering

2010-01-29 Thread rituraj purohit 
Hello friends,

As Justin replied at carla query about structure deformation after the
pdb2gmx & the new number retain till end.

My PDB starts at 24 to 200 aa, While running xmgrace (after complete
simulation) the rmsd plot is from 1 to 176aa.

I understood by previous mail that gromacs renumbered my pdb file at first
step.
My question is, Is their any way to get plot from 24 to 200 (as entry in
pdb) rather 1 to 174 ?

Regard
Rituraj

On Fri, Jan 29, 2010 at 7:28 PM,  wrote:

> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Re: Structure deformation (Carla Jamous)
>   2. Re: Structure deformation (Justin A. Lemkul)
>   3. Re: Re: including a custom itp file in topology (Tsjerk Wassenaar)
>   4. Re: RE: xmgrace (bharat gupta)
>   5. Re: RE: xmgrace (Justin A. Lemkul)
>   6. Re: RE: xmgrace (Baofu Qiao)
>
>
> --
>
> Message: 1
> Date: Fri, 29 Jan 2010 14:03:12 +0100
> From: Carla Jamous 
> Subject: Re: [gmx-users] Structure deformation
> To: jalem...@vt.edu, Discussion list for GROMACS users
>
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you Justin,
> you were right I was looking at the wrong residue numbers.
>
> I have another question that may also sound stupid, but I can't figure it
> out:
> I want to extract from my trajectory, the protein, the ligand and ions.
> However, when I try to do that with trjconv -f .trr -s .trr -n .ndx
> gromacs asks to choose a group from my index file.
> But if I choose group 0 1 2
> it only takes the first group without the rest.
> So how can I extract many groups at once from my trajectory?
>
> Carla
>
> On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul 
> wrote:
>
> >
> >
> > Carla Jamous wrote:
> >
> >> Hi everyone,
> >> I have a question about structure deformation
> >> Can pdb2gmx alter secondary structures of my protein, while adding
> >> hydrogens. Because I had a helix in my protein, that became a beta-sheet
> >> after pdb2gmx.
> >>
> >
> > Sorry to say, but this sounds completely unlikely.  A bug of this
> magnitude
> > surely would've been noticed long ago.
> >
> >
> >  What may be the problem?
> >>
> >>
> > Are you certain you're looking at the same residues?  pdb2gmx renumbers
> > from 1, so if there are missing N-terminal residues, they will not have
> the
> > same numbers  before and after pdb2gmx.
> >
> > -Justin
> >
> >  Thank you
> >> Carla
> >>
> >>
> > --
> > 
> >
> > 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
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.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 gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
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> --
>
> Message: 2
> Date: Fri, 29 Jan 2010 08:04:11 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Structure deformation
> To: "Gromacs Users' List" 
> Message-ID: <4b62dccb.8030...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Carla Jamous wrote:
> > Thank you Justin,
> > you were right I was looking at the wrong residue numbers.
> >
> > I have another question that may also sound stupid, but I can't figure
> > it out:
> > I want to extract from my trajectory, the protein, the ligand and ions.
> > However, when I try to do that with trjconv -f .trr -s .trr -n .ndx
> > gromacs asks to choose a group from my index file.
> > But if I choose group 0 1 2
> > it only takes the first group without the rest.
> > So how can I extract many groups at once from my trajectory?
>
> Use make_ndx to merge the desired groups (i.e., 0 | 1 | 2) or simply !12
> (assuming group 12 is SOL).
>
> -Justin
>
> >
> > Carla
> >
> > On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul  > > wrote:
> >
> >
> >
> > Ca