Re: [gmx-users] dssp 3.1.4

Hi, Do check out gmx do_dssp -h and make sure your dssp binary is the right version, with executable permissions, in the right place (or alternatively the appropriate environment variable is set, so that do_dssp can find dssp) Mark On Fri, 1 May 2020 at 18:47, Iman Katouzian wrote: > Good

[gmx-users] dssp 3.1.4

Good day, I have recently downloaded the latest dssp version and with the mkdssp executable file as I type chmod +x dssp and run this code : gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg -tu ns the process starts but no output is created after even 1 day my

[gmx-users] dssp version of gromacs 2019.3

Good day, I have downloaded the latest version of DSSP from the site : https://swift.cmbi.umcn.nl/gv/dssp/ however as I downloaded and extract the package I see it is named hssp 1.3.4 and the codes are different

Re: [gmx-users] DSSP graph re-scale

Dear Syah, the answer depends on the way you're creating .eps file. I'm assuming that you're using the gmx do_dssp then gmx xpm2ps. something like this can be used: gmx do_dssp -f final.xtc -s my.tpr -n new.ndx -map first.map -tu ns -b 700 -e 1000 -o protein.xpm gmx xpm2ps -f protein.xpm -di

[gmx-users] DSSP graph re-scale

Dear experts, I have an issue to re-scale the x-axis on DSSP graph eps format for my 100 ns simulation time. The x-axis of the graph became too compact until it can't be read clearly. How should I solve this? Is there anyway to re-scale the graph for eps format. Your help is much appreciated.

Re: [gmx-users] dssp error

sometimes it happened if there is any residue that is unknown to DSSP, then it might show this kind of error. I faced it once. On Fri, Mar 22, 2019 at 1:10 AM Mario Andres Rodriguez Pineda < mand...@iq.usp.br> wrote: > I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an >

Re: [gmx-users] dssp error

I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an executable Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao escreveu: > Have a check the installation of DSSP, > did you set the variable DSSP for do_dssp? > > > All the best, > Qinghua > > > On 3/21/19 8:01 PM, Mario

Re: [gmx-users] dssp error

Have a check the installation of DSSP, did you set the variable DSSP for do_dssp? All the best, Qinghua On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote: gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp,

Re: [gmx-users] dssp error

gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option.

Re: [gmx-users] dssp error

Hello, Just follow the suggestion by adding "-ver 2" to your command. All the best, Qinghua On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run

[gmx-users] dssp error

Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program:

Re: [gmx-users] DSSP regardin

Thank you so much Mr Mat. That was very usual. On Sat, Mar 16, 2019 at 10:27 PM Mateusz Bieniek wrote: > Hi Rahul, > > I've run into a similar issue a year ago. It is possible to configure gmx > with the extra configuration file (as described in the documentation) to > get this right. > >

Re: [gmx-users] DSSP regardin

Hi Rahul, I've run into a similar issue a year ago. It is possible to configure gmx with the extra configuration file (as described in the documentation) to get this right. However, I found it to be archaic and wrote my own quick DSSP visualiser in matplotlib. I am planning to improve the code

[gmx-users] DSSP regardin

Hi Users. I have Performed dssp for 1000ns simulation. On converting the xpm to eps, the axis are not visible to any extent. I have tried with different values and I couldn't obtain a good image. Can anyone pass possible suitable commands for long simulations to obtain a satisfactory image? --

Re: [gmx-users] dssp excutable-error

Hi, Have you followed the advice in gmx help do_dssp about setting the environment variables? Did you install the correct version of dssp? Mark On Mon, Nov 12, 2018 at 11:43 PM marzieh dehghan wrote: > Dear all > I installed dssp software on ubuntu version 12.04 in the /usr/local/bin, > when

[gmx-users] dssp excutable-error

Dear all I installed dssp software on ubuntu version 12.04 in the /usr/local/bin, when I run the following command "*sudo find / -name dssp*" it showed the mentioned pathway, but when I apply the following comand "*gmx do_dssp -f xtc -s tpr -o xpm -sc xvg -tu ns*" I confronted to this error:

Re: [gmx-users] DSSP installation

--- > Date: Sat, 9 Dec 2017 11:29:41 +0100 > From: João Henriques <joao.m.a.henriq...@gmail.com> > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] DSSP installation > To: gmx-us...@gromacs.org > > The output is telling you what is wrong. Gro

Re: [gmx-users] DSSP installation

- Message from João Henriques <joao.m.a.henriq...@gmail.com> -     Date: Sat, 9 Dec 2017 11:29:41 +0100     From: João Henriques <joao.m.a.henriq...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] DSSP installation       To: gmx-us...@gromacs.org

Re: [gmx-users] DSSP installation

- Message from João Henriques <joao.m.a.henriq...@gmail.com> -     Date: Sat, 9 Dec 2017 11:29:41 +0100     From: João Henriques <joao.m.a.henriq...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] DSSP installation       To: gmx-us...@gromacs.org

Re: [gmx-users] DSSP installation

The output is telling you what is wrong. Gromacs doesn't support version 3. Install either version 1 or 2. In fact, I didn't even know there was a version 3 of DSSP, where did you get it? It certainly isn't on the official website (http://swift.cmbi.ru.nl/gv/dssp/). J On Fri, Dec 8, 2017 at

[gmx-users] DSSP installation

  Hii all I want to calculate the number of helical contain of protein. For that I tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the tar file and extracted it. Then place the dssp fiolder in /usr/local/bin and exported the path to ./bashrc file export

Re: [gmx-users] DSSP

There's no DSSP version 3 that I know of. That can't be right. J On Tue, Dec 5, 2017 at 5:52 PM, Vidya R wrote: > Hi, > > I have installed dssp version > > > *3.0.0-win32* > > *What should be the command now?* > > On Tue, Dec 5, 2017 at 10:08 PM, João Henriques < >

Re: [gmx-users] DSSP

Hi, Please follow the instructions at gmx do_dssp -h Mark On Wed, Dec 6, 2017, 3:52 AM Vidya R wrote: > Hi, > > I have installed dssp version > > > *3.0.0-win32* > > *What should be the command now?* > > On Tue, Dec 5, 2017 at 10:08 PM, João Henriques < >

Re: [gmx-users] DSSP

Hi, I have installed dssp version *3.0.0-win32* *What should be the command now?* On Tue, Dec 5, 2017 at 10:08 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Did you specify the DSSP version as the error message suggests? DSSP > version 2 has different syntax from the previous

Re: [gmx-users] DSSP

Did you specify the DSSP version as the error message suggests? DSSP version 2 has different syntax from the previous one. On the gromacs 5.1.4 do_dssp assumes that you're using version 2, but maybe yours is version 1. P.S.: I am assuming you have done everything else correctly, i.e., you have a

Re: [gmx-users] DSSP

I got the error dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1# --- Program gmx do_dssp, VERSION 5.1.4 Source code file:

Re: [gmx-users] DSSP

Hi! This is not so much for you as it is for the other users and developers. I think I found a problem with the DSSP code when compiling using the latest boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the "include" directory of this new boost, and the compilation fails. The error

Re: [gmx-users] DSSP

ftp://ftp.cmbi.ru.nl/pub/software/dssp/ There you can find windows .exe version of it. On Tuesday, December 5, 2017, 7:38:44 AM GMT+2, Vidya R wrote: Hi gromacs users, I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.) I want to download and install

[gmx-users] DSSP

Hi gromacs users, I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.) I want to download and install dssp tool. How to proceed? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] dssp plot

Hi Dear all I used dssp plot to show the alteration of secondary structure for special residue numbers such as 100-200, but after calculation them, y axis of dssp plot is started from zero instead from 100. please let me know which part of m2p file should be changed to solve this problem. thanks

Re: [gmx-users] DSSP executable

Thanks Marc! On Mon, Sep 11, 2017 at 6:07 PM, Mark Abraham wrote: > Hi, > > You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first > two > sentences are useful for you ;-) > > Mark > > On Mon, Sep 11, 2017 at 5:05 PM Deep kumar

Re: [gmx-users] DSSP executable

Hi, You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first two sentences are useful for you ;-) Mark On Mon, Sep 11, 2017 at 5:05 PM Deep kumar wrote: > Hello All, > > Can someone please help me get the "dssp" executable? For secondary > structure

[gmx-users] DSSP executable

Hello All, Can someone please help me get the "dssp" executable? For secondary structure analysis. I did this: rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/ This downloaded all dssp pdb files but no executable. I am doing this because I got the error on gromacs run. Fatal error:

Re: [gmx-users] dssp installation using cygwin

Hi, Same as with UNIX. Download the windows binary and teach gmx do_dssp where it is. Mark On Mon, Jun 26, 2017 at 10:26 AM Neha Gupta wrote: > Hi gromacs users, > > I am using gromacs in windows through cygwin > > How to install dssp through cygwin? > > Can anyone

[gmx-users] dssp installation using cygwin

Hi gromacs users, I am using gromacs in windows through cygwin How to install dssp through cygwin? Can anyone help? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] DSSP

On 5/25/17 12:08 PM, Mariusz Wierzbowski wrote: Hi, I would like to analyze secondary structure elements for my protein. I want to do it with do_dssp command in gromacs. I am using gromacs on a plgrid platform. The problem is that an error occurs: Fatal error: DSSP executable

[gmx-users] DSSP

Hi, I would like to analyze secondary structure elements for my protein. I want to do it with do_dssp command in gromacs. I am using gromacs on a plgrid platform. The problem is that an error occurs: Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv DSSP). On

Re: [gmx-users] DSSP

Dear Sir, Now, I have used one single frame by using this command and tried do_dssp trjconv -f md.xtc -o md_1_frame.xtc -b 0 -e 0 do_dssp -s md.tpr -f md_1_frame.xtc -o ss.xpm -sc scount.xvg Now I get the following and this is still going on here are 91 residues in your selected group dssp

Re: [gmx-users] DSSP

On 3/21/17 5:13 AM, Aishwarya Dhar wrote: Following procedure I have used 1. Downloaded http://swift.cmbi.ru.nl/gv/dssp/ dssp-2.0.4-linux-i386 and renamed it dssp 2.made dssp executable and moved it to usr/local/bin 3.Then ran the command from the current location where the tpr and trr

[gmx-users] DSSP

Following procedure I have used 1. Downloaded http://swift.cmbi.ru.nl/gv/dssp/ dssp-2.0.4-linux-i386 and renamed it dssp 2.made dssp executable and moved it to usr/local/bin 3.Then ran the command from the current location where the tpr and trr files are present do_dssp -s md.tpr -f md.trr

[gmx-users] DSSP Erorr

Hi to all first i run 'gmx do_dssp -s md.tpr -f md.xtc' i go this error: Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) then i put dssp executable file in the path 'usr/local/bin/dssp' and run following command : 'export DSSP=/usr/local/bin/dssp' now when i

[gmx-users] DSSP Error

Hi to all first i run 'gmx do_dssp -s md.tpr -f md.xtc' i go this error: Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) then i put dssp executable file in the path 'usr/local/bin/dssp' and run following command : 'export DSSP=/usr/local/bin/dssp' now when i

Re: [gmx-users] DSSP

Hi, gmx do_dssp -h has some useful instructions. Mark On Thu, Jul 7, 2016 at 9:04 AM Sanket Ghawali wrote: > Dear all, > How do i install DSSP for gromacs 5.1.1 > I am curently working on Centos > Which version should i download and any commands to install dssp > >

[gmx-users] DSSP

Dear all, How do i install DSSP for gromacs 5.1.1 I am curently working on Centos Which version should i download and any commands to install dssp Thanks & Regards Sanket -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] DSSP with custom residues

On 4/26/16 1:10 PM, leila salimi wrote: Thanks very much. I have one problem, I am trying to use xpm2ps to plot the secondary structure! I used the m2p file from this link: http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) My problem is that the plot is not

Re: [gmx-users] DSSP with custom residues

Thanks very much. I have one problem, I am trying to use xpm2ps to plot the secondary structure! I used the m2p file from this link: http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) My problem is that the plot is not correct. I tried different xbox and ybox but it

Re: [gmx-users] DSSP with custom residues

Ok. Thank you very much! //Stephanie Den 26 apr 2016 15:00 skrev "Justin Lemkul" : > > > On 4/26/16 8:57 AM, Stephanie Jephthah wrote: > >> Hi! >> >> I'm simulating a protein conjugate and thus uses custom residues. Is there >> any way to make the dssp program aware of the

Re: [gmx-users] DSSP with custom residues

On 4/26/16 9:10 AM, leila salimi wrote: Hi Justin, I am also busy by DSSP analysis. I am interested to know what the difference between do_dssp and dssp is? dssp is a binary that actually carries out the DSSP analysis; it is not a GROMACS program but is downloaded from an external source.

Re: [gmx-users] DSSP with custom residues

Hi Justin, I am also busy by DSSP analysis. I am interested to know what the difference between do_dssp and dssp is? Regards, Leila On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul wrote: > > > On 4/26/16 8:57 AM, Stephanie Jephthah wrote: > >> Hi! >> >> I'm simulating a

Re: [gmx-users] DSSP with custom residues

On 4/26/16 8:57 AM, Stephanie Jephthah wrote: Hi! I'm simulating a protein conjugate and thus uses custom residues. Is there any way to make the dssp program aware of the custom residues (and does it make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm assuming that the

[gmx-users] DSSP with custom residues

Hi! I'm simulating a protein conjugate and thus uses custom residues. Is there any way to make the dssp program aware of the custom residues (and does it make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm assuming that the problem is not with do_dssp but with dssp, but please

Re: [gmx-users] DSSP secondary structure

On 2/15/16 3:26 PM, mohammad r wrote: Thank you Justin, I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any way to calculate the percentage of a-helical structure of a protein during simulation? Indeed DSSP visualize it but I want to calculate it exactly. It

Re: [gmx-users] DSSP secondary structure

Thank you Justin, I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any way to calculate the percentage of a-helical structure of a protein during simulation? Indeed DSSP visualize it but I want to calculate it exactly. Thanks, Mohammad. On Monday, February 15,

Re: [gmx-users] DSSP secondary structure

On 2/15/16 1:31 AM, mohammad r wrote: I changed and reduced the ratio but the xpm file was not changed at all. Unfortunately there's not much I can tell you here because this is rather cryptic. It's illogical to get the same output with different input. You can calculate exactly what

Re: [gmx-users] DSSP secondary structure

I changed and reduced the ratio but the xpm file was not changed at all. On Sunday, February 14, 2016 5:05 PM, Justin Lemkul wrote: On 2/14/16 1:54 AM, mohammad r wrote: > Thank you Justin, > > I used xpm2ps command with below m2p file but the resolution was not

Re: [gmx-users] DSSP secondary structure

On 2/14/16 1:54 AM, mohammad r wrote: Thank you Justin, I used xpm2ps command with below m2p file but the resolution was not changed. I've attached the xpm file, even the legend can't be seen. is there anyway to get the result file in pdf format? m2p file (I found it in the gromacs website):

Re: [gmx-users] DSSP secondary structure

On 2/13/16 1:33 AM, mohammad r wrote: Hi, I used the "gmx do_dssp" command to get the secondary structure of the protein during the simulation but the resolution of the resulted .xpm file is very low. how can I increase its resolution? You can adjust the matrix proportions with an .m2p

Re: [gmx-users] DSSP secondary structure

Thank you Justin, I used xpm2ps command with below m2p file but the resolution was not changed. I've attached the xpm file, even the legend can't be seen.is there anyway to get the result file in pdf format? m2p file (I found it in the gromacs website): black = no ; Obsoletetitlefont =

[gmx-users] DSSP secondary structure

Hi, I used the "gmx do_dssp" command to get the secondary structure of the protein during the simulation but the resolution of the resulted .xpm file is very low. how can I increase its resolution? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] dssp on results of HREX simulation

Dear all, I am getting errors while using do_dssp. I am able to select the main chain for analysis. Following is the error I am getting: *There are 120 residues in your selected groupdssp cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2> /dev/null'Reading frame

Re: [gmx-users] dssp on results of HREX simulation

Dear all, *I was able to fix the error mentioned in the previous message. Here is what I did:* wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O /vega/cheme/users/sm3334/DSSP/dssp chmod a+x /vega/cheme/users/sm3334/DSSP/dssp Modify the .bashrc file export

Re: [gmx-users] dssp on results of HREX simulation

Dear all, wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O /vega/cheme/users/sm3334/DSSP/dssp chmod a+x /vega/cheme/users/sm3334/DSSP/dssp Modify the .bashrc file export DSSP=/vega/cheme/users/sm3334/DSSP/dssp *Now I have a question regarding the secondary structure plot.

Re: [gmx-users] DSSP with gmx 5.0.4

On 03/04/2015 7:36 am, RJ ra...@kaist.ac.kr wrote: Dear gmx users, I tried DSSP of both binary and .exe by renaming it as dssp (dssp-2.0.4-linux-amd64 dssp-2.0.4-win32.exe from ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in usr/local/bin/dssp. Don't try to install a Windows

[gmx-users] DSSP with gmx 5.0.4

Dear gmx users, I tried DSSP of both binary and .exe by renaming it as dssp (dssp-2.0.4-linux-amd64 dssp-2.0.4-win32.exe from ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in usr/local/bin/dssp. set the excusable too ( which dssp /usr/local/bin/dssp). Both of them gives

Re: [gmx-users] DSSP

Dear friend, I think the VMD can do it. Use vmd extension analysis timeline . It will give the residue with color distinguishing which are in sec state with timeframe. But I dont know will it help in finding the percentage of sec. structure. Try it and if u find it how to do, post it here

[gmx-users] DSSP

Hello, Thank you all for your help! I got it working by downloading the executables directly and setting the path but i do get the Program do_dssp, VERSION 5.0 Source code file: /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c, line: 670 Fatal error: Failed to

Re: [gmx-users] DSSP

Have you read and followed gmx do_dssp -h? Mark On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis nm...@york.ac.uk wrote: Hello, Thank you all for your help! I got it working by downloading the executables directly and setting the path but i do get the Program do_dssp, VERSION 5.0

Re: [gmx-users] DSSP

Yes, this is the command i am using: do_dssp -s npt-nopr.tpr -f npt-nopr.trr -o fws-ss.xpm -ver 2 whether i include -ver 2 or not makes no difference, I still get the same error. Cheers, Nicholas On 25 August 2014 15:53, Mark Abraham mark.j.abra...@gmail.com wrote: Have you read and

Re: [gmx-users] DSSP

check the permissions of dssp executables and give the execute permission if it is not already. *Thanks and Regards,Bipin Singh* On Mon, Aug 25, 2014 at 6:26 PM, Nikolaos Michelarakis nm...@york.ac.uk wrote: Yes, this is the command i am using: do_dssp -s

[gmx-users] DSSP

Hello, I am trying to do a secondary structure analysis to get the percentages of each secondary structure in my protein. I know i can use do_dssp but unfortunately DSSP is not installed on the cluster that i have been using and i do not have the acess to install it. Any other ways to do it? or

Re: [gmx-users] DSSP

You may use the precompiled dssp executables. *Thanks and Regards,Bipin Singh* On Mon, Aug 25, 2014 at 5:31 AM, Nikolaos Michelarakis nm...@york.ac.uk wrote: Hello, I am trying to do a secondary structure analysis to get the percentages of each secondary

Re: [gmx-users] DSSP

Hi, Thank you for your answer, could you please give me some more info on where to find them and how to use them for the whole trajectory? Cheers, Nicholas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] DSSP

You may download the relevant executables from the following links: ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-win32.exe before using the do_dssp module of Gromacs,

Re: [gmx-users] dssp

Hi Uma, What happens if you run dssp by itself on the command line? Cheers, Tsjerk On Fri, Jun 6, 2014 at 5:13 AM, Uma Devi renuma...@gmail.com wrote: Thanks Mr. Erik for your kind reply. yes the file name is dssp.exe only On Thu, Jun 5, 2014 at 3:10 PM, Uma Devi renuma...@gmail.com

Re: [gmx-users] dssp

HI please check version of the dssp that ur trying to use on CentOS. It could be the case that its a window exec file ur trying to run on linux.. thank you Gurunath On Fri, Jun 6, 2014 at 11:35 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Uma, What happens if you run dssp by itself on

[gmx-users] dssp

dear sir/madam i am new to gromacs. i am trying to install DSSP,i am having centos. i downloaded the DSSP and pasted it in /usr/local/bin directory while i am running it shows the following error Failed to execute command: /usr/local/bin/dssp.exe -na ddLV8RKo ddvXmynp /dev/null 2 /dev/null

Re: [gmx-users] dssp

Hi, dssp.exe? Are you sure that's the name of the file? Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 5 Jun 2014, at 10:40, Uma Devi

Re: [gmx-users] dssp

Thanks Mr. Erik for your kind reply. yes the file name is dssp.exe only On Thu, Jun 5, 2014 at 3:10 PM, Uma Devi renuma...@gmail.com wrote: dear sir/madam i am new to gromacs. i am trying to install DSSP,i am having centos. i downloaded the DSSP and pasted it in /usr/local/bin directory

Re: [gmx-users] dssp installation error

Hi, A: Did you set the DSSP environment variable to the dssp executable? B: Does your dssp version match that which is expected by do_dssp? Yours, Erik On 10 May 2014, at 19:39, elham tazikeh elham.tazi...@gmail.com wrote: dear gromacs users when i run do_dssp program 4.5 and 4.6 i saw

[gmx-users] dssp installation error

dear gromacs users when i run do_dssp program 4.5 and 4.6 i saw below error plz help me progran do_dssp, version 4.5.3 source code file:do_dsso.c, line: 521 fatal error: failed to execute command: /usr/local/bin/dssp -na dd5iLsk0 ddj8721A /dev/null2 /dev/null best regards elham tazikeh --