[gmx-users] do_dssp fatal error
Paymon Pirzadeh
ppirzade at ucalgary.ca
Wed Oct 6 18:51:50 CEST 2010
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 <roman at chem.ubc.ca>
> > Date:
> > Tue, 5 Oct 2010 19:31:23 -0700 (PDT)
> > To:
> > Paymon Pirzadeh <ppirzade at ucalgary.ca>
> >
> > To:
> > Paymon Pirzadeh <ppirzade at 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:roman at 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
>
> ========================================
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