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/[EMAIL PROTECTED]/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/[EMAIL PROTECTED]/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
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]

_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to