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.
>>>
>>>
>>>
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>
>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
>
>========================================
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--
Nuno Gonçalo Azoia Lopes
Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal
Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293
Mobile: +351 965 382 487
E-mail: [EMAIL PROTECTED]
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