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 your comments
2013/3/1 Erik Marklund <er...@xray.bmc.uu.se> > 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 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 <er...@xray.bmc.uu.se> >> >> 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 ddQ3PqtX -o ddR1HavD > /dev/null 2> >>>> /dev/null' >>>> Reading frame 0 time 0.000 >>>> Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# >>>> >>>> ------------------------------****------------------------- >>>> Program do_dssp, VERSION 4.6 >>>> Source code file: /usr/local/bin/gromacs-4.6/**** >>>> src/tools/gmx_do_dssp.c, >>>> >>>> line: >>>> 667 >>>> >>>> Fatal error: >>>> Failed to execute command: Try specifying your dssp version with the >>>> -ver >>>> option. >>>> >>>> How can I fix that? >>>> >>>> Thanks >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 2013/1/15 James Starlight <jmsstarli...@gmail.com> >>>> >>>> Justin, thanks both options works perfect. >>>> >>>>> >>>>> >>>>> James >>>>> >>>>> 2013/1/15 Justin Lemkul <jalem...@vt.edu>: >>>>> >>>>> >>>>>> >>>>>> 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 contents (though they are usually somewhat unclear when >>>>>> >>>>>> plotted >>>>> >>>>> together) with xmgrace -nxy scount.xvg >>>>>> >>>>>> >>>>>> By the way have you forced with some problems with dppc ? Simetimes >>>>>> >>>>>>> I've obtain error like >>>>>>> >>>>>>> >>>>>>> There are 286 residues in your selected group >>>>>>> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2> >>>>>>> /dev/null' >>>>>>> Reading frame 0 time 0.000 >>>>>>> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 >>>>>>> >>>>>>> >>>>>>> Fatal error: >>>>>>> Failed to execute command: Try specifying your dssp version with the >>>>>>> -ver option. >>>>>>> >>>>>>> and I dont know how to fix it. >>>>>>> >>>>>>> I'm using gromacs-4.6-beta 3 with dssp 2.0.3 >>>>>>> >>>>>>> >>>>>>> Since dssp changed its command line options, Gromacs had to adapt as >>>>>> >>>>>> well. >>>>> >>>>> The error tells you to use the -ver option; you should do so. >>>>>> Version 2 >>>>>> should be the default, so check to make sure you're actually using >>>>>> that >>>>>> version and not the old dssp. >>>>>> >>>>>> >>>>>> -Justin >>>>>> >>>>>> -- >>>>>> ==============================****========== >>>>>> >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Research Scientist >>>>>> Department of Biochemistry >>>>>> Virginia Tech >>>>>> Blacksburg, VA >>>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>>>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>>>>> > >>>>>> >>>>>> ==============================****========== >>>>>> >>>>>> -- >>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>> > >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/****Support/Mailing_Lists/Search<http://www.gromacs.org/**Support/Mailing_Lists/Search> >>>>>> <h**ttp://www.gromacs.org/Support/**Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>>>> posting! >>>>>> >>>>>> * Please don't post (un)subscribe requests to the list. 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