[gmx-users] do_dssp fatal error
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 6 18:41:23 CEST 2010
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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