Re: [gmx-users] do_dssp

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 of

Re: [gmx-users] do_dssp

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 wrote: > I am facing problem while using do

[gmx-users] do_dssp

I am facing problem while using do_dssp.I -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the lis

Re: [gmx-users] do_dssp

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 dec

Re: [gmx-users] do_dssp

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 for

Re: [gmx-users] do_dssp

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 I

Re: [gmx-users] do_dssp

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

Re: [gmx-users] do_dssp

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 change that? 2013/3/1 Erik Marklund > What happens i

Re: [gmx-users] do_dssp

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 ddQ3Pqt

Re: [gmx-users] do_dssp

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 > /de

[gmx-users] do_dssp with 4.6

Dear gmx users, Has anyone tried dssp-2.1.0 with gromacs-4.6? I am having the common problems that were supossed not to be in the new releases -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.

Re: [gmx-users] do_dssp

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# ---

Re: [gmx-users] do_dssp

Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul : > > > 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

Re: [gmx-users] do_dssp

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 its

Re: [gmx-users] do_dssp

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

Re: [gmx-users] do_dssp

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 simul

[gmx-users] do_dssp

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 simulation ? By the way during analysis of the graph

Re: [gmx-users] do_dssp Segmentation fault

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

Re: [gmx-users] do_dssp Segmentation fault

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

[gmx-users] do_dssp Segmentation fault

Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environm

Re: [gmx-users] do_dssp segmental fault

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 chm

[gmx-users] do_dssp segmental fault

Dear gmx users, I recently upgraded the operating system to Ubuntu 12 and re-installed Gromacs 4.5.5. But I could not re-install dssp. I did the following: (1) I downloaded dsspcmbi from http://swift.cmbi.ru.nl/gv/dssp/ Went to distributions- DSSPold - Linux Distributions to download dsspcmbi. (2)

Re: [gmx-users] do_dssp segmentation fault error

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

[gmx-users] do_dssp segmentation fault error

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 precision) Reading file md.tpr, VERSION

Re: [gmx-users] do_dssp

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

Re: [gmx-users] do_dssp

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: "c

Re: [gmx-users] do_dssp

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 ga

[gmx-users] do_dssp

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 the user the right to e

Re: [gmx-users] do_dssp segmentation fault

On 3/03/2012 6:21 PM, arun kumar wrote: yes other gromacs tools are working properly ...i installed gromacs in /usr/local/ so i used the command /usr/local/gromacs/bin/./do_dssp -s md.tpr -f md.xtc -o ss.xpm and i also set the environment variable as export DSSP=/usr/local/gromacs/bin/do_dssp

Re: [gmx-users] do_dssp segmentation fault

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

[gmx-users] do_dssp segmentation fault

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 fault (core dumped) bash-4.1# can anybody p

Re: [gmx-users] do_dssp segmentation fault

, do a ./bootstrap before the configure step. Best, Carsten > > Bests > > Da: Carsten Kutzner > A: Alex Jemulin ; Discussion list for GROMACS users > > Inviato: Martedì 22 Novembre 2011 13:25 > Oggetto: Re: [gmx-users] do_dssp segmentation fault > > Dear Alex, &g

Re: [gmx-users] do_dssp segmentation fault

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 > se

Re: [gmx-users] do_dssp segmentation fault

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?

[gmx-users] do_dssp segmentation fault

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? Thank in ad-- gmx-users mailing listgmx-

[gmx-users] do_dssp normalization error

Dear Gromacs users, I used do_dssp to calculate the secondary structure of peptide. From the output scount.xvg file, the last column shows the number of residues that is "chain separator". At the end of the scount.xvg file, the last line provide the percentage of different secondary struc

Re: [gmx-users] do_dssp

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 com

[gmx-users] do_dssp

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 compile the CMBI version of DSSP,

[gmx-users] DO_DSSP

Thank you very much! Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www i

Re: [gmx-users] DO_DSSP

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

[gmx-users] DO_DSSP

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 >> 2.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp#./D

Re: [gmx-users] do_dssp failed to execute

Sunita Patel wrote: *** *Dear Mark, On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote > - Original Message - > From: Sunita Patel > Date: Monday, October 11, 2010 22:50 > Subject: [gmx-users] do_dssp failed to execute > To: Discussion list for GROMACS user

Re: [gmx-users] do_dssp failed to execute

Dear Mark, On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote > - Original Message - > From: Sunita Patel > Date: Monday, October 11, 2010 22:50 > Subject: [gmx-users] do_dssp  failed to execute > To: Discussion list for GROMACS users > > > Dear User, >

Re: [gmx-users] do_dssp failed to execute

- Original Message - From: Sunita Patel Date: Monday, October 11, 2010 22:50 Subject: [gmx-users] do_dssp failed to execute To: Discussion list for GROMACS users > Dear User, > > I set the path for dssp executable in .bashrc file. Still dssp in the path is probably not s

[gmx-users] do_dssp failed to execute

Dear User, I set the path for dssp executable in .bashrc file. Still getting following error. Could anybody suggest what would be the problem. error message Select a group: 5 Selected 5: 'MainChain' There are 134 residues in your selected group Opening lib

Re: [gmx-users] do_dssp fatal error

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:

Re: [gmx-users] do_dssp fatal error

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 the

[gmx-users] do_dssp fatal error

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 the archive to select the alph

Re: [gmx-users] do_dssp

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 det

Re: [gmx-users] do_dssp

Hi No i dont have any capping group shahid Nayeem On 5/24/10, Justin A. Lemkul 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

Re: [gmx-users] do_dssp

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* > wrote: shahid nayeem wrote: Dear All I did 10n

Re: [gmx-users] do_dssp

Hi Justin I choose group 5 main chain for dssp calculation Shahid Nayeem On 5/24/10, Justin A. Lemkul 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 showin

Re: [gmx-users] do_dssp

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 g

[gmx-users] do_dssp

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 get total residue as 80. The

Re: [gmx-users] do_dssp

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 shel

[gmx-users] do_dssp

Hi dear Justin The executable is dssp leila karami -- 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

Re: [gmx-users] do_dssp

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. > >

Re: [gmx-users] do_dssp

OK. you are right! Rasoul On Wed, Jan 6, 2010 at 1:09 PM, Justin A. Lemkul wrote: > > > 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

Re: [gmx-users] do_dssp

yes. Could you perform do_dssp properly? Rasoul On Wed, Jan 6, 2010 at 1:05 PM, leila karami wrote: > 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 > http://lists.gromacs.o

Re: [gmx-users] do_dssp

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 its

[gmx-users] do_dssp

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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

Re: [gmx-users] do_dssp

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 loca

Re: [gmx-users] do_dssp

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 t

Re: [gmx-users] do_dssp

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 wrote: > dear Rasoul > > I had executable dssp program, already. > > leila karami > > -- > gmx-

[gmx-users] do_dssp

dear Rasoul I had executable dssp program, already. leila karami -- 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.

Re: [gmx-users] do_dssp

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 wrote: > Hi > > I apply following command: > > do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map > > but

[gmx-users] do_dssp

Hi I apply following command: do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map but following error is came up: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddal9qL4 ddRvmyo0 > /dev/null 2> /dev/null Any help will highly appreciated! -- gmx-users mailing listgmx-user

Re: [gmx-users] do_dssp Installation instructions in case you have errors

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 unde

[gmx-users] do_dssp Installation instructions in case you have errors

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 understand after hours fiddling

Re: [gmx-users] do_dssp question

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 no

[gmx-users] do_dssp question

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 not sure if I need to download

Re: [gmx-users] do_dssp fatal error

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 and

[gmx-users] do_dssp fatal error

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 and adjust the .bashrc. w

Re: [gmx-users] do_dssp fatal error

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 execu

[gmx-users] do_dssp fatal error

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 execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro > /dev/null 2> /dev/null How could I fix this. Thank you in advance. -- Tehran University o

Re: [gmx-users] do_dssp

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 plot.ep

[gmx-users] do_dssp

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 plot.eps file I get the followin

Re: [gmx-users] do_dssp

Morteza Khabiri wrote: Dear florian thanks for your help. I installed the DSSP in the root. It is working well when I run ./dssp in DSSP directory. It seems that the program don't have any problem. As you said I already set an environment also but any of them did not working. It made me crazy tha

[gmx-users] do_dssp

Dear florian thanks for your help. I installed the DSSP in the root. It is working well when I run ./dssp in DSSP directory. It seems that the program don't have any problem. As you said I already set an environment also but any of them did not working. It made me crazy that everything is ok, Insta

Re: [gmx-users] do_dssp

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

[gmx-users] do_dssp

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 it will be finished and also after running I have a message which

Re: [gmx-users] do_dssp

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.

Re: [gmx-users] do_dssp

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 availa

Re: Re: [gmx-users] do_dssp

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 tell

Re: [gmx-users] do_dssp

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 secon

Re: [gmx-users] do_dssp

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. W

[gmx-users] do_dssp

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. I am bit confusing

[gmx-users] do_dssp file format, Resolved !!!

Hi Gromacs Users My Problem with do_dssp is resolved : my do_dssp was strangely corrupted. After recompilation it works well. Thank you for all people who helped me. See U soon on this mailing list Stefane ___ gmx-users mailing listgmx-users@grom

Re: [gmx-users] do_dssp file format

ABEL Stephane 175950 wrote: Yes, Mark i have taken a look in your previous message To test my dssp program I took a pdb from the protein data bank: 1HRC. This pdb contains only one protein (and one frame). The DSSP program works fine with it and I obtain an output. So To test my do_dssp i also

[gmx-users] do_dssp file format

Yes, Mark i have taken a look in your previous message To test my dssp program I took a pdb from the protein data bank: 1HRC. This pdb contains only one protein (and one frame). The DSSP program works fine with it and I obtain an output. So To test my do_dssp i also used this pdb. In this case

Re: [gmx-users] do_dssp file format

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 p

[gmx-users] do_dssp file format

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 protein configuration in it)

Re: [gmx-users] do_dssp file format

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 see

Re: [gmx-users] do_dssp file format

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 Stephan

Re: [gmx-users] do_dssp file format

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,

[gmx-users] do_dssp file format

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 GROningen MAchine for Chemical Simulation :-) VERSION 3.3.1 (-: Written by

Re: [gmx-users] do_dssp file format

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=contents&Page=1 > Boîte de réception > > As suggested David and others i rename my pdb file with the extension .pdb > > i use

[gmx-users] do_dssp file format

My story with do_dssp continues...https://webmail.cea.fr/Exchange/Stephane.ABEL/Bo%C3%AEte%20de%20r%C3%A9ception/?Cmd=contents&Page=1 Boîte de réception As suggested David and others i rename my pdb file with the extension .pdb i used the following command ./do_dssp -s RM106-Cytc-CH22-SecStr

Re: [gmx-users] do_dssp file format

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

[gmx-users] do_dssp file format

11.641 -5.923 -13.130 -0.76 0.00 ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 -- Message: 3 Date: Thu, 10 Jan 2008 13:03:30 -0500 From: "Justin A. Lemkul" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] do_dss

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