Re: [gmx-users] do_dssp Segmentation fault

2012-11-12 Thread Erik Marklund
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

2012-11-12 Thread João Henriques
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

2012-11-11 Thread mshappy1986
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 segmentation fault error

2012-05-16 Thread Justin A. Lemkul
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

2012-05-16 Thread bunty xy
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 segmentation fault

2012-03-02 Thread Mark Abraham
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

2012-03-02 Thread Mark Abraham
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

2012-03-02 Thread arun kumar
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

2011-11-23 Thread Carsten Kutzner
, 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

2011-11-22 Thread Carsten Kutzner
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

2011-11-22 Thread Mark Abraham
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

2011-11-22 Thread Alex Jemulin
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-