[gmx-users] do_dssp fatal error

2010-10-06 Thread Paymon Pirzadeh
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

Re: [gmx-users] do_dssp fatal error

2010-10-06 Thread Justin A. Lemkul
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

Re: [gmx-users] do_dssp fatal error

2010-10-06 Thread Paymon Pirzadeh
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:

[gmx-users] do_dssp fatal error

2009-03-17 Thread Homa Azizian
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.

Re: [gmx-users] do_dssp fatal error

2009-03-17 Thread Justin A. Lemkul
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

[gmx-users] do_dssp fatal error

2009-03-10 Thread Homa Azizian
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 of

Re: [gmx-users] do_dssp fatal error

2009-03-10 Thread Diego Enry Gomes
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