Re: [gmx-users] about do_dssp

[Justin A. Lemkul]

babu gokul wrote:

dear all
I am analyzing  a collagen dynamics i would like to analysis the 
collagen structure in and its parameter ? what is the difference between 
beta bridge and beta strand.




I would suggest you have a look at the DSSP paper.

http://www.gromacs.org/Developer_Zone/Programming_Guide/DSSP

-Justin

thank you 
E R azhagiya singam




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] about do_dssp

[Tsjerk Wassenaar]

Hi hazizian,

That information is stored in the file you get with the option -sc. To
get percentages you have to use awk or something along thos lines.

Cheers,

Tsjerk

On Tue, Jul 14, 2009 at 5:47 AM, hazizian wrote:
>
> Hi
> I have a question about do_dssp program.is it posible to define the amount
> of residus (the percentage) which have specific secondry structure, apart
> from the graphic file? if yes what is the the command?
> Thanks
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> ___
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.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 gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php