[gmx-users] do_dssp

[Nuno Azoia]

Maybe I can help with some more details. I'm sorry if my explanation is 
to much detailed.

I start to use do_dssp a few days ago. I went to the website Justin just 
mentioned and I just downloaded the binary file. I copy that file to 
/usr/local/bin
The binary file that I downloaded is dsspcmbi. So, before try do_dssp I 
create a soft link "dssp" to the binary dsspcmbi. I've created the link 
in the same directory (/usr/local/bin), and everything is just work fine.

Nuno Azoia



Justin A. Lemkul wrote:
>
>
> minnale wrote:
>>  
>> Thanks for the reply Justin
>> I tried like this
>> do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str
>> it has given
>> Fatal error:
>> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
>>
>
> The prerequisite is a separate (non-Gromacs) program called DSSP.  It 
> is available here:
>
> http://swift.cmbi.ru.nl/gv/dssp/
>
> Install dssp into /usr/local/bin and try do_dssp again.
>
> -Justin
>
>> I checked with archives do_dssp is a seperate program and install 
>> separately,
>> Could you pls tell me how can I install do_dssp program or is there 
>> anyway to calculate  secondary structure of protein?
>> Thanks in advance.
>>
>>
>> On Fri, 15 Aug 2008 Justin A.Lemkul wrote :
>>  >
>>  >As a final note, it is probably better to use the .xtc file for 
>> analysis.  The do_dssp program is very slow, and I can only imagine 
>> that reading the full-precision trajectory will slow to an absolute 
>> crawl.
>>  >
>>  >-Justin
>>  >
>>  >Justin A. Lemkul wrote:
>>  >>
>>  >>
>>  >>minnale wrote:
>>  >>>  Hi all,
>>  >>>  I want to analyse secondary struture of my protein which have 
>> run MD for 7ns. I have checked in archives about do_dssp, found that 
>> can use only .pdb file instead of .trr and .tpr. Then if type command 
>> with -h it has it has given .xtc, .tpr,  and .ndx should use.
>>  >>
>>  >>Where does it say that you can't use your trajectory?  That's 
>> certainly incorrect.  The standalone dssp program (which you must 
>> obtain separately from the DSSP site) can only run on a single .pdb 
>> file, but Gromacs makes use of the dssp executable such that it can 
>> be used with trajectories.
>>  >>
>>  >>Hence the lovely plots you see in the literature.
>>  >>
>>  >>-Justin
>>  >>
>>  >>>I am bit confusing with about do_dssp command.
>>  >>>Can you explain me clearly. Thanks in advance.
>>  >>>
>>  >>>
>>  >>>
>>  >>>Rediff Shopping 
>> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null> 
>>
>>
>>  >
>>  >Justin A. Lemkul
>>  >Graduate Research Assistant
>>  >Department of Biochemistry
>>  >Virginia Tech
>>  >Blacksburg, VA
>>  >jalemkul[at]vt.edu | (540) 231-9080
>>  >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>  >
>>  >========================================
>>
>>
>>
>> Rediff Shopping 
>> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null> 
>>
>>
>


-- 

Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
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Portugal

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E-mail: nazoia at det.uminho.pt