Re: [gmx-users] DSSP output

[Justin Lemkul]

On 11/7/13 8:24 AM, Anirban wrote:

Hi ALL,

Is there any way to get the percentage of each secondary structural content
of a protein using do_dssp if I supply a single PDB to it?


The output of scount.xvg has the percentages, but it's also trivial to do it for 
one snapshot.  The contents of scount.xvg are the number of residues present in 
each type of secondary structure, and you know the total number of residues...



And how to plot the data of the -sc output from do_dssp?


Like any multiple data set.  xmgrace -nxy

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] DSSP output

[Anirban]

Hi ALL,

Is there any way to get the percentage of each secondary structural content
of a protein using do_dssp if I supply a single PDB to it?
And how to plot the data of the -sc output from do_dssp?
Any suggestion is welcome.

Regards,

Anirban
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Re: [gmx-users] dssp output of CG structure of 1K4C

[sunny mishra]

OK. Thanks a lot justin

On Tue, Aug 18, 2009 at 1:16 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Hi Justin,
>>
>> Thanks for the expedient reply. So in that case I cannot get the dssp
>> output of my CG structure for sure. So in that case do I have to get the
>> .ssd files of my 1K4C_clean.pdb file only right and then get the .seq file
>> of 1K4c_clean.pdb in order to proceed. Am I right?
>>
>>
> Right, to generate the MARTINI topology you need both .ssd and .seq files.
>
> -Justin
>
>  Sunny
>>
>>
>> On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>sunny mishra wrote:
>>
>>Dear all,
>>
>>I wanted to get the dssp output of Coarse Grained structure of
>>my protein i.e. 1K4C. In order to get that I have a script which
>>is given to me in the MARTINI tutorial (dssp2ssd.py). I have
>>also downloaded the dssp successfully in my linux machine. In my
>>first step i cleaned the 1K4C protein and renamed it as
>>1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title
>>and atoms with C ligands in it. When i convert the
>>1K4C_clean.pdb to CG structure using atom2CG script with the
>>help of awk command I get the CG structure successfully and I
>>renamed it 1K4C_cleancg.pdb. But when I am trying to get the
>>dssp output of 1K4C_cleancg.pdb using dssp it produces nothing
>>but on the other hand it produces the dssp output of my normal
>>cleaned 1K4C pdb file. Do you know if there is anyway I can get
>>the dssp output of my CG structure of protein?
>>
>>
>>Not likely.  DSSP calculates secondary structure from hydrogen
>>bonds, which will be absent in a CG model.  The script you refer to
>>(dssp2ssd.py) does not use DSSP to calculate secondary structure; it
>>simply converts DSSP output to the .ssd file needed by MARTINI.
>>
>>-Justin
>>
>>Thanks,
>>
>>Sunny
>>
>>
>>
>>  
>>
>>___
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>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>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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>>
>>
>>
>> 
>>
>> ___
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] dssp output of CG structure of 1K4C

[Justin A. Lemkul]

sunny mishra wrote:

Hi Justin,

Thanks for the expedient reply. So in that case I cannot get the dssp 
output of my CG structure for sure. So in that case do I have to get the 
.ssd files of my 1K4C_clean.pdb file only right and then get the .seq 
file of 1K4c_clean.pdb in order to proceed. Am I right?




Right, to generate the MARTINI topology you need both .ssd and .seq files.

-Justin


Sunny

On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

Dear all,

I wanted to get the dssp output of Coarse Grained structure of
my protein i.e. 1K4C. In order to get that I have a script which
is given to me in the MARTINI tutorial (dssp2ssd.py). I have
also downloaded the dssp successfully in my linux machine. In my
first step i cleaned the 1K4C protein and renamed it as
1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title
and atoms with C ligands in it. When i convert the
1K4C_clean.pdb to CG structure using atom2CG script with the
help of awk command I get the CG structure successfully and I
renamed it 1K4C_cleancg.pdb. But when I am trying to get the
dssp output of 1K4C_cleancg.pdb using dssp it produces nothing
but on the other hand it produces the dssp output of my normal
cleaned 1K4C pdb file. Do you know if there is anyway I can get
the dssp output of my CG structure of protein?


Not likely.  DSSP calculates secondary structure from hydrogen
bonds, which will be absent in a CG model.  The script you refer to
(dssp2ssd.py) does not use DSSP to calculate secondary structure; it
simply converts DSSP output to the .ssd file needed by MARTINI.

-Justin

Thanks,

Sunny




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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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
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] dssp output of CG structure of 1K4C

[sunny mishra]

Hi Justin,
Thanks for the expedient reply. So in that case I cannot get the dssp output
of my CG structure for sure. So in that case do I have to get the .ssd files
of my 1K4C_clean.pdb file only right and then get the .seq file of
1K4c_clean.pdb in order to proceed. Am I right?

Sunny

On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Dear all,
>>
>> I wanted to get the dssp output of Coarse Grained structure of my protein
>> i.e. 1K4C. In order to get that I have a script which is given to me in the
>> MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully
>> in my linux machine. In my first step i cleaned the 1K4C protein and renamed
>> it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and
>> atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG
>> structure using atom2CG script with the help of awk command I get the CG
>> structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am
>> trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces
>> nothing but on the other hand it produces the dssp output of my normal
>> cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp
>> output of my CG structure of protein?
>>
>>
> Not likely.  DSSP calculates secondary structure from hydrogen bonds, which
> will be absent in a CG model.  The script you refer to (dssp2ssd.py) does
> not use DSSP to calculate secondary structure; it simply converts DSSP
> output to the .ssd file needed by MARTINI.
>
> -Justin
>
>  Thanks,
>>
>> Sunny
>>
>>
>> 
>>
>> ___
>> 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!
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>> interface or send it to gmx-users-requ...@gromacs.org.
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>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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!
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>
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Re: [gmx-users] dssp output of CG structure of 1K4C

[Justin A. Lemkul]

sunny mishra wrote:

Dear all,

I wanted to get the dssp output of Coarse Grained structure of my 
protein i.e. 1K4C. In order to get that I have a script which is given 
to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the 
dssp successfully in my linux machine. In my first step i cleaned the 
1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists 
only the header title and atoms with C ligands in it. When i convert the 
1K4C_clean.pdb to CG structure using atom2CG script with the help of awk 
command I get the CG structure successfully and I renamed it 
1K4C_cleancg.pdb. But when I am trying to get the dssp output of 
1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it 
produces the dssp output of my normal cleaned 1K4C pdb file. Do you know 
if there is anyway I can get the dssp output of my CG structure of protein?




Not likely.  DSSP calculates secondary structure from hydrogen bonds, which will 
be absent in a CG model.  The script you refer to (dssp2ssd.py) does not use 
DSSP to calculate secondary structure; it simply converts DSSP output to the 
.ssd file needed by MARTINI.


-Justin


Thanks,

Sunny




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] dssp output of CG structure of 1K4C

[sunny mishra]

Dear all,
I wanted to get the dssp output of Coarse Grained structure of my protein
i.e. 1K4C. In order to get that I have a script which is given to me in the
MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully
in my linux machine. In my first step i cleaned the 1K4C protein and renamed
it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and
atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG
structure using atom2CG script with the help of awk command I get the CG
structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am
trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces
nothing but on the other hand it produces the dssp output of my normal
cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp
output of my CG structure of protein?

Thanks,

Sunny
___
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