[gmx-users] Re: gmx-users Digest, Vol 52, Issue 66

[minnale]

Thanks Nuno for your information , the archives mentioned website about  do_dssp it's not freely available program. I couldnt able to get the program, am I right Could please help me.
Thanks alot

>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
> >>  >
> >>  >========================================
> >>
> >>
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