Re: [gmx-users] Structure deformation

[Carla Jamous]

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
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Re: [gmx-users] Structure deformation

[Justin A. Lemkul]

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:




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


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--


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


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Re: [gmx-users] Structure deformation

[Justin A. Lemkul]

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


--
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[gmx-users] Structure deformation

[Carla Jamous]

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.
What may be the problem?

Thank you
Carla
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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