Preeti,
if do_dssp doesn't work for you, try to do it manually using the following web
service:
http://www.cmbi.ru.nl/hsspsoap/
I use it because my platform (MAC OSX) can't run DO_DSSP
Best of luck!
On May 14, 2013, at 11:00 AM, Preeti Choudhary
preetichoudhary18111...@gmail.com wrote:
I
On 5/14/13 11:11 AM, Xu Dong Huang wrote:
Preeti,
if do_dssp doesn't work for you, try to do it manually using the following web
service:
http://www.cmbi.ru.nl/hsspsoap/
I use it because my platform (MAC OSX) can't run DO_DSSP
I've used dssp/do_dssp on Mac for years. It's all a matter
Hi,
I'll try out the 2.1.0 with do_dssp and see if there's something
problematic with this new version. Good thing you brought it up.
Erik
On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote:
Hi Erik,
Since I read in the mailing list that nobody had asked about 2.1.0,
just
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2
/dev/null'
Reading frame 0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#
With -ver, just like it says. do_dssp -h explains how. What dssp
version do you have?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD
What happens if you execute the command (/usr/local/bin/dssp/ -i
ddQ3PqtX -o ddR1HavD) in your terminal?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i
On 3/1/13 11:16 AM, Miguel Ángel Mompeán García wrote:
The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works
fine. However, when converting the xpm to eps I get I plot very small,
where one barely can see the colour code and the legend is sooo big. Does
anyone know how to
Interesting. Perhaps there are new issues with 2.1.0. Did you try to
execute the command yourself?
Erik
On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:
The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and
it works
fine. However, when converting the xpm to eps
Hi Erik,
Since I read in the mailing list that nobody had asked about 2.1.0, just
decided to try an older version before going into the trouble itself...
Kind of coward, I know, but the troubles with that version are already
reported so that I thought things would be easier :)
Thank-you a lot
On 1/15/13 3:19 AM, James Starlight wrote:
Dear Gromacs Users!
I'd like to know if it's possible to obtain some values from do_dssp
except the graph diagrams of the ss dynamics ? For example I wounder
to know values of how many residues were in helix, sheet or coil
conformation during my
Justin,
I want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By default that graph has not legend so it's hard
to analyse it .
By the way have you forced with some problems with dppc ? Simetimes
I've obtain error like
There are 286 residues in your selected
On 1/15/13 7:13 AM, James Starlight wrote:
Justin,
I want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By default that graph has not legend so it's hard
to analyse it .
The legends are printed in the .xvg header. I've never had a problem plotting
Justin, thanks both options works perfect.
James
2013/1/15 Justin Lemkul jalem...@vt.edu:
On 1/15/13 7:13 AM, James Starlight wrote:
Justin,
I want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By default that graph has not legend so it's hard
to
Hello,
do_dssp (4.5.5) is broken. There are two possible answers you're gonna get
here:
1) Use old dssp, which you are using.
2) You're an idiot, which are not.
What I did to solve the problem was, download gmx from git, and substitute
the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the
Hi,
The explanation is that DSSP changed its syntax some time ago and do_dssp no
longer complied. More recent versions of do_dssp follows the new syntax while
still supporting the old one.
Erik
12 nov 2012 kl. 10.55 skrev João Henriques:
Hello,
do_dssp (4.5.5) is broken. There are two
Hi Deb,
I recently installed dssp for Gromacs 4.5.4 on RHEL4
You have to just copy the dsspcmbi downloaded from linux distribution to
/usr/local/bin (No need to set an environment variable DSSP if dspcmbi is
in /usr/loca/bin as it is the default path for gromacs)
Rename the dsspcmbi to dssp
On 5/16/12 5:57 AM, bunty xy wrote:
Hello Friends
I have installed GROMACS 4.5.5 on linux.
I put the DSSP Executable in /usr/local/bin
when i run the following command:
do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm
i got the following error.
Reading file md.tpr, VERSION 4.5.5 (single
Bernhard Knapp wrote:
Hi
I have some problems to get do_dssp running:
I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ .
Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I copied
it to the correct location: cp dssp-2-linux-i386 /usr/local/bin/dssp
and gave
On 4/04/2012 10:02 PM, Justin A. Lemkul wrote:
Bernhard Knapp wrote:
Hi
I have some problems to get do_dssp running:
I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/
. Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I
copied it to the correct location: cp
Bernhard Knapp wrote:
The problem with this solution is that I would have to recompile gromacs
on all maschines were I want to use dssp, right? Is there an older
version of dssp still available from somewhere? On the dssp-homepage I
found unfortunatly only the current but no past versions of
On 3/03/2012 5:14 PM, arun kumar wrote:
Dear all,
Iam trying to generate secondary structure plot through do_dssp
program, but there was an error like segmentation fault
Reading file md.tpr, VERSION 4.0.7 (single precision)
Reading file md.tpr, VERSION 4.0.7 (single precision)
Segmentation
before the configure step.
Best,
Carsten
Bests
Da: Carsten Kutzner ckut...@gwdg.de
A: Alex Jemulin alexbioi...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Inviato: Martedì 22 Novembre 2011 13:25
Oggetto: Re: [gmx-users] do_dssp segmentation fault
Dear
On 22/11/2011 7:28 PM, Alex Jemulin wrote:
Dear all
I'm experiencing the following error in Gromacs 4.5 with do_dssp
Here is the command
do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg -dt 10
give me the following error
segmentation fault
How can I fix it?
Dear Alex,
On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote:
Dear all
I'm experiencing the following error in Gromacs 4.5 with do_dssp
Here is the command
do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg -dt 10
give me the following error
afsaneh maleki wrote:
Hi,
I'm trying to use do_dssp of gromacs 4.5.4 in fedora core .
I did processes of Download , Uncompress and Compile the source code as
the following
unzip dsspcmbi.zip
cd dssp
[root@localhost dssp]# ./DsspCompileGCC
That i got this message:
Running script to
On 6/05/2011 5:22 PM, battis...@libero.it wrote:
Dear all,
I'm trying install do_dssp on my pc.
I followed the steps indicated in the page:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html
1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf
dsspcmbi.tar.gz
- Original Message -
From: Sunita Patel sun...@mailhost.tifr.res.in
Date: Monday, October 11, 2010 22:50
Subject: [gmx-users] do_dssp failed to execute
To: Discussion list for GROMACS users gmx-users@gromacs.org
Dear User,
I set the path for dssp executable in .bashrc file. Still
Dear Mark,
On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote
- Original Message -
From: Sunita Patel sun...@mailhost.tifr.res.in
Date: Monday, October 11, 2010 22:50
Subject: [gmx-users] do_dssp failed to execute
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sunita Patel wrote:
***
*Dear Mark,
On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote
- Original Message -
From: Sunita Patel sun...@mailhost.tifr.res.in
Date: Monday, October 11, 2010 22:50
Subject: [gmx-users] do_dssp failed to execute
To: Discussion list for GROMACS
Paymon Pirzadeh wrote:
Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:
do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265
Then, I had read somewhere in
Dear Justin,
Thanks a lot. Your comment was very instructive. So, I use Mainchain
(group 5) for future.
Paymon
On Wed, 2010-10-06 at 12:41 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:
shahid nayeem wrote:
Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is showing
total 78 residue which is O.K. as 3x26=78. For inserting three similar
peptide I used genconf command. when I run dssp I
Hi Justin
I choose group 5 main chain for dssp calculation
Shahid Nayeem
On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote:
shahid nayeem wrote:
Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is
shahid nayeem wrote:
Hi Justin
I choose group 5 main chain for dssp calculation
Do you have any capping groups (N-acetyl, C-amine, etc)?
-Justin
Shahid Nayeem
On 5/24/10, *Justin A. Lemkul* jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
shahid nayeem wrote:
Dear All
Hi
No i dont have any capping group
shahid Nayeem
On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote:
shahid nayeem wrote:
Hi Justin
I choose group 5 main chain for dssp calculation
Do you have any capping groups (N-acetyl, C-amine, etc)?
-Justin
Shahid Nayeem
On 5/24/10,
shahid nayeem wrote:
Hi
No i dont have any capping group
Then I have no idea what's going on. The only data that present a problem are
in the very first frame, indicating that the HEBT+coil content totals 80
residues. All the other frames look fine. It could be that the algorithm is
Do you have a DSSP program on your system? If no, please install executable
DSSP program from http://swift.cmbi.kun.nl/gv/dssp/ website.
Rasoul
On Wed, Jan 6, 2010 at 11:34 AM, leila karami karami.lei...@gmail.comwrote:
Hi
I apply following command:
do_dssp -f rrr.xtc -s .tpr -n n.ndx
Then your executable has problem. Gromacs tool can not find DSSP for doing
d_dssp. Do you put executable DSSP in the path of gromacs is installed?
Rasoul.
On Wed, Jan 6, 2010 at 11:58 AM, leila karami karami.lei...@gmail.comwrote:
dear Rasoul
I had executable dssp program, already.
leila
On 1/6/10 5:58 AM, leila karami wrote:
dear Rasoul
I had executable dssp program, already.
Then have you set your PATH appropriately, as well as the DSSP environment
variable? See the help information for do_dssp to see the assumptions that the
program is making regarding the location of
On 1/6/10 6:57 AM, rasoul nasiri wrote:
Then your executable has problem. Gromacs tool can not find DSSP for
doing d_dssp. Do you put executable DSSP in the path of gromacs is
installed?
This is not necessary. One needs to set the environment variable DSSP
correctly, since the default
On 1/6/10 7:05 AM, leila karami wrote:
dear Rasoul
I put executable DSSP in /usr/local/bin and gromacs is
in /usr/local/gromacs.
is it true?
Is the executable named DSSP, or dssp? Case matters. DSSP is the environment
variable that must be set, while dssp is the name of the executable
yes. Could you perform do_dssp properly?
Rasoul
On Wed, Jan 6, 2010 at 1:05 PM, leila karami karami.lei...@gmail.comwrote:
dear Rasoul
I put executable DSSP in /usr/local/bin and gromacs is
in /usr/local/gromacs.
is it true?
--
gmx-users mailing listgmx-users@gromacs.org
Hi Leila!
Can I add just one more note?
The file dssp, that you put in the right place, has the permissions to
be executed?
Nuno Azoia
On Wed, 2010-01-06 at 15:35 +0330, leila karami wrote:
dear Rasoul
I put executable DSSP in /usr/local/bin and gromacs is
in /usr/local/gromacs.
is
On 1/6/10 7:52 AM, leila karami wrote:
Hi
dear Justin
The executable is dssp
leila karami
Do you have the correct mode set for the executable (i.e., is it actually
executable)? Did you use a pre-compiled binary, or compile it yourself from
source? If you issue which dssp does your shell
Kirill Bessonov wrote:
I had seen people having trouble with do_dssp and that Error line 471
error.
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null
2 /dev/null
So I would like to spill some light on the issue and make documentation
better to
Kirill Bessonov wrote:
I have used do_dssp program to analyze secondary structure during
simulation of DMPC/DMPE. But I am not clear on installation of dssp.
The program seems to work, I have set all the environmental variables so
that dssp binary is seen in /home/DSSP directory, but I am
Homa Azizian wrote:
Hi
thanks Dr. van der Spoel my previous problem fixed.
I have another question.
I download DSSP from http://swift.cmbi.ru.nl/gv/dssp/ from the part
Distribution in the left partition of the page. it was the zip file and I
unzip it and positioned it in my /usr/local/bin
Did you download the dssp software from here ?
http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
On Mar 10, 2009, at 1:12 AM, Homa Azizian wrote:
Hi
when I use do_dssp the following error come:
Program do_dssp, VERSION 4.0.3
Source code file: do_dssp.c, line: 471
Fatal error:
Failed to
Morteza Khabiri wrote:
Dear gmxuser,
I ried the do_dssp command to analyses my protein structure. It produce
scount.xvg ans ss.xpm file. I could see xvg file by xmgrace and ss,xpm by
GIMP software. Till now everything is ok. But when I want a make post
script file by xpm2ps for producing
Hi,
On Wednesday, 29. October 2008, Morteza Khabiri wrote:
Dear gmx users,
I run the program do_dssp for my system which is too small. Unfortunately,
I run it for a long time but I am in a doubt that it is working correctly
or not
because it is run for one day and i don't have any idea when
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.
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
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)
I checked with archives do_dssp is a seperate program and install separately,
Could you pls
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
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.
ABEL Stephane 175950 wrote:
Hi Gromacs users
After many try this weekend with my problem with do_dssp I come back to the mailing list
First, as David said me last friday in a previous message I have test my dssp
program with example of pdb file from the Protein Data Bank (1HRC) (with one
Quoting ABEL Stephane 175950 [EMAIL PROTECTED]:
My story with do_dssp
continues...https://webmail.cea.fr/Exchange/Stephane.ABEL/Bo%C3%AEte%20de%20r%C3%A9ception/?Cmd=contentsPage=1
Boîte de réception
As suggested David and others i rename my pdb file with the extension .pdb
i used the
ABEL Stephane 175950 wrote:
I am back :(
The procedure i did
1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm
The menu appears I choose 5 (Main Chain) and I obtained the following message
try running normal dssp first
dssp pdbfile
to see if dssp works
--
David van der Spoel,
Is it a single structure in the .pdb file? Or is it many frames of a
trajectory? It is noted in the manual that do_dssp is very slow. In my
experience (on my laptop), I can analyze 5 frames in roughly 3 hours. Are
you waiting long enough for do_dssp to finish?
-Justin
Quoting ABEL
ABEL Stephane 175950 wrote:
I am back :(
The procedure i did
1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm
The menu appears I choose 5 (Main Chain) and I obtained the following message
The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But the program
Quoting ABEL Stephane 175950 [EMAIL PROTECTED]:
Hi gromacs users
For my work I have performed some simulations of a protein in water with an
other MD software not compatible with GROMACS. And I would like to compute
the time evolution of the secondary structure of my protein, I know that
ABEL Stephane 175950 wrote:
I used the following command
./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault.
Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and
ABEL Stephane 175950 wrote:
Hi gromacs users
For my work I have performed some simulations of a protein in water with an
other MD software not compatible with GROMACS. And I would like to compute the
time evolution of the secondary structure of my protein, I know that the
do_dssp tool in
Volker Knecht wrote:
Dear all,
Does anyone have an idea what is going wrong?
No, but it would straightforward to write a script that used trjconv
while iterating through a set of index files that extract the
coordinates of just one peptide at a time, write that to an intermediate
.xtc
Hi,
perhaps your .trr has some errors. Have you tried converting it or gmxcheck?
Other solution could be: Transfer your protein residues to an multiple pdb
file and try do_dssp again. Perhaps your top or ndx doesn't fit.
On Wednesday, 23. May 2007 17:07, Volker Knecht wrote:
Dear all,
[EMAIL PROTECTED] wrote:
Dear community,
I have the following problem with do_dssp, when I try analysing a long 70 ns
trajectory produced by a REMD calculation. All my previous analysis went fine,
when the trajectory had a length of ~= 50ns. However, I now obtain the following
errror message,
hi,
On Thursday, 19. April 2007 17:23, Mark Abraham wrote:
[EMAIL PROTECTED] wrote:
Dear community,
I have the following problem with do_dssp, when I try analysing a long 70
ns trajectory produced by a REMD calculation. All my previous analysis
went fine, when the trajectory had a
singh wrote:
Dear Gromacs users,
As I am simulating many peptides in a box and do_dssp is only a wrapper for
calling the program which works on pdb files, I was of the view that it will
not take PBC into consideration and will probably not assign beta sheets
very well. Please correct me if I am
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Jahan,
First, you must make sure you have the dssp program; it doesn't come
with gromacs, but you can download it separately from:
http://swift.cmbi.ru.nl/gv/dssp/
Secondly, if 'setenv' is not working you are not on a csh/tcsh shell. Try:
Thanks for your reply. I used from Gromacs on WindowsXP with command prompt. How can I change DSSP path in this environment? Thank you very much.Sincerely yours, JahanMiguel Ortiz Lombardia [EMAIL PROTECTED] wrote: -BEGIN PGP SIGNED MESSAGE-Hash: SHA1Hi Jahan,First, you must make
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