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 <[email protected]>
Date:
Tue, 5 Oct 2010 19:31:23 -0700 (PDT)
To:
Paymon Pirzadeh <[email protected]>
To:
Paymon Pirzadeh <[email protected]>
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:[email protected]]
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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