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: > > > > 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 alpha carbons > > for accurate results, and I did, but the following error pops up: > > > > Then you read an inaccurate post. At the very least, all MainChain atoms > must > be considered. Think about how the DSSP algorithm works - assessment of > hydrogen bonding patterns. Can these patterns be determined by using only > alpha > carbons? > > I know I have posted several times about how to properly use do_dssp, and it > is > also on the wiki: > > http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp > > > Program do_dssp_d_mpi, VERSION 4.0.5 > > Source code file: do_dssp.c, line: 471 > > > > Fatal error: > > Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na > > ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null > > > > The cluster technician tested the forwarded procedure (appended below), > > and it seems that the backbone structure has some problems. I will be > > appreciated if one tells me is it really a problem with backbone or sth > > with installation of dssp. If problem is with backbone, then why pdb2gmx > > did not issue any warnings? > > The results below indicate that the command works correctly for groups that > contain all the necessary atoms. Failures only occur when other, incorrect, > groups are used. > > -Justin > > > Regards, > > > > Paymon > > > > > > ------------------------------------------------------------------------ > > > > Subject: > > RE: Sorry + Re: GROMACS utilities > > From: > > Roman Baranowski <ro...@chem.ubc.ca> > > Date: > > Tue, 5 Oct 2010 19:31:23 -0700 (PDT) > > To: > > Paymon Pirzadeh <ppirz...@ucalgary.ca> > > > > To: > > Paymon Pirzadeh <ppirz...@ucalgary.ca> > > > > > > > > Dear Paymon, > > > > I have interrupted the run (it was taking too long) and I did not want > > to prevent you from work in that directory. For: > > Opening library file > > /global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat > > Group 0 ( System) has 293280 elements > > Group 1 ( Protein) has 1002 elements > > Group 2 ( Protein-H) has 485 elements > > Group 3 ( C-alpha) has 66 elements > > Group 4 ( Backbone) has 198 elements > > Group 5 ( MainChain) has 265 elements > > Group 6 (MainChain+Cb) has 328 elements > > Group 7 ( MainChain+H) has 327 elements > > Group 8 ( SideChain) has 675 elements > > Group 9 ( SideChain-H) has 220 elements > > Group 10 ( Prot-Masses) has 1002 elements > > Group 11 ( Non-Protein) has 292278 elements > > Group 12 ( SOL) has 292278 elements > > Group 13 ( Other) has 292278 elements > > > > 0,1,2,5,6,7 work but > > 3,4,8,9,10,11,12 and 13 do not. However the output > > Fatal error: > > Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na > > ddNPsTyg dda8k3CK > > suggests that there is some problem with the input. So tried to run > > dssp -na ddNPsTyg dda8k3CK > > interactively (without do_dssp_d_mpi -f AFPIII .......) and: > > > > dssp -na ddNPsTyg dda8k3CK > > (I have used the full path i.e.: > > /global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP) > > > > the output is (I remove most of the lines as they do not seem to be > > relevant): > > !!! Backbone incomplete for residue ALA 1 > > residue will be ignored !!! > > > > !!! Backbone incomplete for residue ASN 2 > > residue will be ignored !!! > > > > !!! Backbone incomplete for residue GLN 3 > > residue will be ignored !!! > > ....................... > > ...................... > > > > !!! Backbone incomplete for residue ALA 66 > > residue will be ignored !!! > > > > !!! HEADER-card missing !!! > > !!! COMPOUND-card missing !!! > > !!! SOURCE-card missing !!! > > !!! AUTHOR-card missing !!! > > !!! No residue with complete backbone !!! > > > > So it once again suggests the input issue. I do not know too much about > > Gromacs and dssp setup but it clearly points to input. > > > > All the best > > Roman > > > > > > > > On Tue, 5 Oct 2010, Paymon Pirzadeh wrote: > > > >> Dear Roman, > >> do_dssp does analysis on secondary structure of proteins. It is written > >> on online blogs that to get the correct results, you should select alpha > >> carbons, option 3. However, the only problem that might be the case is > >> providing an index file of backbone alpha carbones which looks > >> irrelevant since do_dssp asks about the group interactively. I don't > >> know if I can try the command or not (since you mentioned it is > >> running), but you may try it again with group option 3. > >> Regards, > >> > >> Paymon > >> > >> > >> On Tue, 2010-10-05 at 16:40 -0700, Roman Baranowski wrote: > >>> > >>> Dear Paymon, > >>> > >>> I have just log in as you, cd to: > >>> GROMACS/proteins/AFP-III/Ih0001/81_93_204/AFPIII_Ih0001_81_93_NpT265_round1 > >>> > >>> > >>> and issued > >>> module load gromacs > >>> and than: > >>> 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 > >>> > >>> Select a group: 0 > >>> Selected 0: 'System' > >>> There are 48779 residues in your selected group > >>> Opening library file > >>> /global/software/gromacs/4.0.5/intel/share/gromacs/top/ss.map > >>> Reading frame 0 time 0.000 > >>> Back Off! I just backed up ddOjBDfr to ./#ddOjBDfr.1# > >>> Reading frame 1 time 10.000 > >>> Reading frame 50 time 500.000 > >>> > >>> and it is still running , is it possible that there is a need for some > >>> extra maps or databases used by dssp in the share directory. > >>> > >>> All the best > >>> Roman > >>> > >>> > >>> On Tue, 5 Oct 2010, Paymon Pirzadeh wrote: > >>> > >>>> Dear Roman, > >>>> I tried it again and the still same error: > >>>> > >>>> Program do_dssp_d_mpi, VERSION 4.0.5 > >>>> Source code file: do_dssp.c, line: 471 > >>>> > >>>> Fatal error: > >>>> Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na > >>>> dd4qT1kw ddhRhEOb > /dev/null 2> /dev/null > >>>> > >>>> The command I used was > >>>> > >>>> 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 > >>>> > >>>> The location of files are: > >>>> > >>>> /global/home/pirzadeh/GROMACS/proteins/AFP-III/Ih0001/81_93_204/AFPIII_Ih0001_81_93_NpT265_round1 > >>>> > >>>> > >>>> > >>>> I should say that each each time I rerun "module load gromacs". > >>>> Regards, > >>>> > >>>> Paymon > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> On Tue, 2010-10-05 at 14:23 -0700, Roman Baranowski wrote: > >>>>> > >>>>> Dear Paymon, > >>>>> > >>>>> Please try again, at the same time, Please send me the full command > >>>>> which > >>>>> gives you this error (point me to your input and output files etc). > >>>>> > >>>>> All the best > >>>>> Roman > >>>>> > >>>>> > >>>>> On Tue, 5 Oct 2010, Paymon Pirzadeh wrote: > >>>>> > >>>>>> Dear Roman, > >>>>>> There is still problems: > >>>>>> > >>>>>> Program do_dssp_d_mpi, VERSION 4.0.5 > >>>>>> Source code file: do_dssp.c, line: 471 > >>>>>> > >>>>>> Fatal error: > >>>>>> Failed to execute command: /global/software/gromacs/dssp/bin -na > >>>>>> ddOgL0Rd ddqM7KPo > /dev/null 2> /dev/null > >>>>>> > >>>>>> Regards, > >>>>>> > >>>>>> Paymon > >>>>>> > >>>>>> > >>>>>> > >>>>>> On Tue, 2010-10-05 at 13:55 -0700, Roman Baranowski wrote: > >>>>>>> > >>>>>>> Dear Paymon, > >>>>>>> > >>>>>>> Can you please try again. I think I solve the issue (the binary code > >>>>>>> downloaded has to be removed and the new has been just built from > >>>>>>> the > >>>>>>> source). > >>>>>>> > >>>>>>> All the best > >>>>>>> Roman > >>>>>>> > >>>>>>> On Tue, 5 Oct 2010, Paymon Pirzadeh wrote: > >>>>>>> > >>>>>>>> Dear Roman, > >>>>>>>> I tried to run the do_dssp_d_mpi 4.0.5, here is the error: > >>>>>>>> > >>>>>>>> Program do_dssp_d_mpi, VERSION 4.0.5 > >>>>>>>> Source code file: do_dssp.c, line: 471 > >>>>>>>> > >>>>>>>> Fatal error: > >>>>>>>> Failed to execute command: /global/software/gromacs/dssp/bin -na > >>>>>>>> ddP9udW0 ddBWjBu5 > /dev/null 2> /dev/null > >>>>>>>> > >>>>>>>> I am not sure what the error is talking about. I expected dssp be a > >>>>>>>> single file in the bin forlder, but it looks different here! > >>>>>>>> Sorry for inconveniences. > >>>>>>>> regards, > >>>>>>>> > >>>>>>>> Paymon > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> On Mon, 2010-10-04 at 17:54 -0700, Roman Baranowski wrote: > >>>>>>>>> > >>>>>>>>> Dear Paymon, > >>>>>>>>> > >>>>>>>>> Sorry for the delay the dssp has been installed (I am still > >>>>>>>>> downloading > >>>>>>>>> the database and it should be done shortly). In order to use > >>>>>>>>> do_dssp_d_mpi > >>>>>>>>> do_dssp_d do_dssp_s etc. please reload the appropriate gromacs > >>>>>>>>> module > >>>>>>>>> (gromacs/4.0.7-serial or gromacs/4.0.7 for 4.0.7 version, or > >>>>>>>>> 4.0.5). > >>>>>>>>> Please let me know if all is working as expected. > >>>>>>>>> > >>>>>>>>> All the best > >>>>>>>>> Roman > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> On Mon, 4 Oct 2010, Payman Pirzadeh wrote: > >>>>>>>>> > >>>>>>>>>> Dear Roman, > >>>>>>>>>> Have you had a chance to look into the DSSP issue of GROMACS I > >>>>>>>>>> e-mailed > >>>>>>>>>> about last week? > >>>>>>>>>> Sorry for mass of e-mails. > >>>>>>>>>> Regards, > >>>>>>>>>> > >>>>>>>>>> Paymon > >>>>>>>>>> > >>>>>>>>>> -----Original Message----- > >>>>>>>>>> From: Roman Baranowski [mailto:ro...@chem.ubc.ca] > >>>>>>>>>> Sent: October 1, 2010 2:37 AM > >>>>>>>>>> To: Payman Pirzadeh > >>>>>>>>>> Subject: Sorry + Re: GROMACS utilities > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> Dear Paymon, > >>>>>>>>>> > >>>>>>>>>> I will look into this (do_dssp_d_mpi utility) issue later today. > >>>>>>>>>> > >>>>>>>>>> Now a little bit embarrassing mistake, editing the quota I > >>>>>>>>>> made an error > >>>>>>>>>> and did not modify properly your quota on orcinus it was still > >>>>>>>>>> at 400G > >>>>>>>>>> your jobs are generating quite a lot of data and your usage > >>>>>>>>>> hit this level > >>>>>>>>>> as a result the jobs on orcinus exited. I hope you can > >>>>>>>>>> continue with the > >>>>>>>>>> last checkpoint. Pleas resubmit and I will increase your > >>>>>>>>>> priority so they > >>>>>>>>>> will start asap. My apologies.... > >>>>>>>>>> > >>>>>>>>>> All the best > >>>>>>>>>> Roman > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> On Thu, 30 Sep 2010, Payman Pirzadeh wrote: > >>>>>>>>>>> > >>>>>>>>>>> Dear Roman, > >>>>>>>>>>> > >>>>>>>>>>> I tried to use the do_dssp_d_mpi utility of GROMACS and it > >>>>>>>>>>> did not > >>>>>>>>>> work. It turned out that the executable file is not in the bin > >>>>>>>>>> file > >>>>>>>>>>> based on the error message: > >>>>>>>>>>> > >>>>>>>>>>> Regards, > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> Paymon > >>>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>> > >>>>>>> > >>>>>>> > >>>>>> > >>>>> > >>>>> > >>>> > >>> > >>> > >> > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > 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 Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists