Shahid, Before trying for "do_dssp" a gromacs utility calling dssp program , try first dssp program itself by passing simple input like pdb and I hope by that way you can resolve your problem B.Nataraj -----Original Message----- From: [email protected] [mailto:[email protected]]on Behalf Of shahid nayeem Sent: Tuesday, May 18, 2010 5:17 PM To: [email protected]; Discussion list for GROMACS users Subject: Re: [gmx-users] DSSP Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem
On 5/18/10, Justin A. Lemkul < [email protected]> wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is "dsspcmbi," which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at] vt.edu <http://vt.edu/> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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