Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Sudip Das 
Hi Justin,

Thanks a lot for your reply!! I got my answer from that link.

Best wishes,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Thu, Dec 14, 2017 at 1:09 AM, Justin Lemkul  wrote:

>
>
> On 12/13/17 1:40 PM, Sudip Das wrote:
>
>> Hi Justin,
>>
>> Thanks again for your valuable time!
>>
>> The sasa output file I got contains only two columns (time and sasa).
>>
>> The output coordinate for protein is matching neither with the reference
>> coordinate (from .tpr file), nor with the first or last frame.
>>
>> I am using the following command:
>>
>> gmx_mpi sasa -f traj.xtc -s topol.tpr -n index.ndx -o sasa -q surface.pdb
>> -surface
>>
>> Am I doing something wrong?
>>
>
> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_
> for_5.0?highlight=tool+changes+for+5.0#g_sas
>
>
> -Justin
>
> --
> ==
>
> 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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Justin Lemkul 



On 12/13/17 1:40 PM, Sudip Das wrote:

Hi Justin,

Thanks again for your valuable time!

The sasa output file I got contains only two columns (time and sasa).

The output coordinate for protein is matching neither with the reference
coordinate (from .tpr file), nor with the first or last frame.

I am using the following command:

gmx_mpi sasa -f traj.xtc -s topol.tpr -n index.ndx -o sasa -q surface.pdb
-surface

Am I doing something wrong?


http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0?highlight=tool+changes+for+5.0#g_sas

-Justin

--
==

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.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Sudip Das 
Hi Justin,

Thanks again for your valuable time!

The sasa output file I got contains only two columns (time and sasa).

The output coordinate for protein is matching neither with the reference
coordinate (from .tpr file), nor with the first or last frame.

I am using the following command:

gmx_mpi sasa -f traj.xtc -s topol.tpr -n index.ndx -o sasa -q surface.pdb
-surface

Am I doing something wrong?


Best wishes,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Dec 13, 2017 at 11:23 PM, Justin Lemkul  wrote:

>
>
> On 12/13/17 12:50 PM, Sudip Das wrote:
>
>> Dear Justin,
>>
>> Thanks for your reply!
>>
>> As you said, I checked with gmx sasa. But it is giving total SASA for the
>> selected region of protein, not the hydrophobic and hydrophilic part of
>> the
>> total SASA for that region. To get it, do I have to use some flags
>> available with gmx sasa?
>>
>
> The output should be a multi-column file, IIRC, but it has been years
> since I've used it.
>
> I have one more query. When I specified -surface flag with gmx sasa, I got
>> the coordinate for the protein together with the coordinate for surface
>> area as dotted point. I have done this calculation over 50 to 100 ns of my
>> simulation trajectory. Is the generated coordinate for protein
>> (together with the coordinate for dotted surface area) averaged over all
>> the frames within 50 to 100ns?
>>
>
> I assume it's just pulling the reference coordinates from the .tpr file,
> but you'd have to check the code to see what it's doing to be sure.
>
>
> -Justin
>
> --
> ==
>
> 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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Sudip Das 
Dear Rahul,

Thanks for your reply!

Best wishes,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Dec 13, 2017 at 9:56 PM, RAHUL SURESH 
wrote:

> Hi Sudip
>
> I am not sure if you can do that for the entire trajectory but for a pdb
> structure at particular ns you can calculate the hydrophobicity of
> particular part of protein using Discovery studio.(You have to adopt some
> backbench tricks)
>
> Thank you
>
> On Wed, Dec 13, 2017 at 9:52 PM, Sudip Das  wrote:
>
> > Dear All,
> >
> > Is there any tool available that can calculate hydrophobic and
> hydrophilic
> > (solvent accessible) surface areas *for a particular portion (not the
> > whole)* of a protein?
> >
> > Thanks in advance!
> >
> > Best wishes,
> >
> > Sudip Das
> >
> > PhD Student
> > C/o. Prof. S. Balasubramanian
> > Molecular Simulations Lab
> > Chemistry and Physics of Materials Unit (CPMU)
> > Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> > Bangalore, 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.
>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Justin Lemkul 



On 12/13/17 12:50 PM, Sudip Das wrote:

Dear Justin,

Thanks for your reply!

As you said, I checked with gmx sasa. But it is giving total SASA for the
selected region of protein, not the hydrophobic and hydrophilic part of the
total SASA for that region. To get it, do I have to use some flags
available with gmx sasa?


The output should be a multi-column file, IIRC, but it has been years 
since I've used it.



I have one more query. When I specified -surface flag with gmx sasa, I got
the coordinate for the protein together with the coordinate for surface
area as dotted point. I have done this calculation over 50 to 100 ns of my
simulation trajectory. Is the generated coordinate for protein
(together with the coordinate for dotted surface area) averaged over all
the frames within 50 to 100ns?


I assume it's just pulling the reference coordinates from the .tpr file, 
but you'd have to check the code to see what it's doing to be sure.


-Justin

--
==

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.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Sudip Das 
Dear Justin,

Thanks for your reply!

As you said, I checked with gmx sasa. But it is giving total SASA for the
selected region of protein, not the hydrophobic and hydrophilic part of the
total SASA for that region. To get it, do I have to use some flags
available with gmx sasa?

I have one more query. When I specified -surface flag with gmx sasa, I got
the coordinate for the protein together with the coordinate for surface
area as dotted point. I have done this calculation over 50 to 100 ns of my
simulation trajectory. Is the generated coordinate for protein
(together with the coordinate for dotted surface area) averaged over all
the frames within 50 to 100ns?

Thanks again for your valuable time.

Best wishes,
Sudip


‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Dec 13, 2017 at 10:12 PM, Justin Lemkul  wrote:

>
>
> On 12/13/17 11:22 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> Is there any tool available that can calculate hydrophobic and hydrophilic
>> (solvent accessible) surface areas *for a particular portion (not the
>> whole)* of a protein?
>>
>
> Yes, you can get that from gmx sasa. Generate a surface for the whole
> protein, and choose whatever subset of that surface that you want as the
> output.
>
> -Justin
>
> --
> ==
>
> 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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
> --
> 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] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Justin Lemkul 



On 12/13/17 11:22 AM, Sudip Das wrote:

Dear All,

Is there any tool available that can calculate hydrophobic and hydrophilic
(solvent accessible) surface areas *for a particular portion (not the
whole)* of a protein?


Yes, you can get that from gmx sasa. Generate a surface for the whole 
protein, and choose whatever subset of that surface that you want as the 
output.


-Justin

--
==

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.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread RAHUL SURESH 
Hi Sudip

I am not sure if you can do that for the entire trajectory but for a pdb
structure at particular ns you can calculate the hydrophobicity of
particular part of protein using Discovery studio.(You have to adopt some
backbench tricks)

Thank you

On Wed, Dec 13, 2017 at 9:52 PM, Sudip Das  wrote:

> Dear All,
>
> Is there any tool available that can calculate hydrophobic and hydrophilic
> (solvent accessible) surface areas *for a particular portion (not the
> whole)* of a protein?
>
> Thanks in advance!
>
> Best wishes,
>
> Sudip Das
>
> PhD Student
> C/o. Prof. S. Balasubramanian
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit (CPMU)
> Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> Bangalore, 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.




-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

2017-12-13 Thread Sudip Das 
Dear All,

Is there any tool available that can calculate hydrophobic and hydrophilic
(solvent accessible) surface areas *for a particular portion (not the
whole)* of a protein?

Thanks in advance!

Best wishes,

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India



‌
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