[gmx-users] Regarding DSSP
Mark Abraham
mark.j.abraham at gmail.com
Tue Feb 17 06:41:04 CET 2015
Hi,
Exactly what dssp command worked? Your use of do_dssp must be consistent
with that. You must be making a specific error, so general descriptions of
your actions are likely to be counterproductive. :-) Please don't filter
things through your head, because that assumes you are doing the right
things, and the evidence is against that! :-)
Mark
On Feb 17, 2015 1:14 AM, "HANNIBAL LECTER" <hanniballecter13 at gmail.com>
wrote:
>
> Yes, the binary is working on a single pdb file.
>
> On Mon, Feb 16, 2015 at 7:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 2/16/15 6:55 PM, HANNIBAL LECTER wrote:
> >
> >> Sorry, yes, I actually made a copy and pasted in the /usr/bin
directory as
> >> well. So there IS actually a copy of the same program.
> >>
> >> Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit
> >> version as well. Same error as above.
> >>
> >>
> > Does the dssp binary work when you run it on a single .pdb file (as it's
> > designed to do)? If not, then the binary is (somehow) incompatible with
> > your machine. Compiling from source would fix that.
> >
> > -Justin
> >
> > On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 2/16/15 6:40 PM, HANNIBAL LECTER wrote:
> >>>
> >>> Okay. what can be possibly wrong? I mean if someone CAN run
> >>>> Gromacs-5.0.4
> >>>> +
> >>>> DSSP 2.0.4, it should be running in other systems as well unless I am
> >>>> messing something up. So I list my steps.
> >>>>
> >>>> 1. Download the executable from
> >>>> ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source
code,
> >>>> but
> >>>> just the binaries).
> >>>>
> >>>> 2. rename the file to dssp204
> >>>> 3. chmod +x dssp204
> >>>> 4. sudo mv dssp204 /usr/local/bin/
> >>>> 5. export DSSP=/usr/loca/bin/dssp204
> >>>> 6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2
> >>>>
> >>>> What can be possibly wrong?
> >>>>
> >>>>
> >>>> Not sure, because what you're telling us isn't consistent:
> >>>
> >>> 1. You're not copying and pasting (or you are and you're setting
> >>> variables
> >>> wrong) because step 4 shows "/usr/loca/bin" as the location of the
> >>> executable, which in step 3 you (presumably) put in /usr/local/bin
(which
> >>> actually makes sense).
> >>>
> >>> 2. That's not what you did because:
> >>>
> >>> dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i > /dev/null 2>
> >>> /dev/null'
> >>>
> >>> says you have installed something called "dssp20464" in /usr/bin.
> >>>
> >>> It's hard to troubleshoot something when you're not giving us
consistent
> >>> information. If the suffix "20464" indicates version "2.0.4" and
64-bit
> >>> architecture, is that appropriate for your system? You have a 64-bit
> >>> system, not 32-bit?
> >>>
> >>> -Justin
> >>>
> >>>
> >>> The output is shown below:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single
> >>>> precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6
> >>>> (single precision)Group 0 ( System) has 10901
elementsGroup
> >>>> 1 ( Protein) has 121 elementsGroup 2 ( Protein-H)
has
> >>>> 68 elementsGroup 3 ( C-alpha) has 16 elementsGroup
4
> >>>> ( Backbone) has 50 elementsGroup 5 ( MainChain) has
> >>>> 67
> >>>> elementsGroup 6 ( MainChain+Cb) has 67 elementsGroup 7 (
> >>>> MainChain+H) has 85 elementsGroup 8 ( SideChain) has
36
> >>>> elementsGroup 9 ( SideChain-H) has 1 elementsGroup 10 (
> >>>> Prot-Masses) has 121 elementsGroup 11 ( non-Protein) has
10780
> >>>> elementsGroup 12 ( Other) has 2320 elementsGroup 13
> >>>> ( RS1) has 2320 elementsGroup 14 ( Water) has
> >>>> 8460
> >>>> elementsGroup 15 ( SOL) has 8460 elementsGroup 16 (
> >>>> non-Water) has 2441 elementsSelect a group: 1Selected 1:
'Protein'There
> >>>> are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i
> >>>> ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame 0
time
> >>>> 0.000 Back Off! I just backed up ddUkWy9e to
> >>>> ./#ddUkWy9e.1#----------------------------------------------
> >>>> ---------Program
> >>>> gmx, VERSION 5.0.4Source code file:
> >>>>
> >>>>
/home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
> >>>> line: 670Fatal error:Failed to execute command: Try specifying your
dssp
> >>>> version with the -ver option.For more information and tips for
> >>>> troubleshooting, please check the GROMACSwebsite at
> >>>> http://www.gromacs.org/Documentation/Errors
> >>>> <http://www.gromacs.org/Documentation/Errors>---------
> >>>> ----------------------------------------------*
> >>>>
> >>>>
> >>>> On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul <jalemkul at vt.edu>
wrote:
> >>>>
> >>>>
> >>>>
> >>>>> On 2/16/15 6:20 PM, HANNIBAL LECTER wrote:
> >>>>>
> >>>>> Okay, so the same errors seem to be persisting.
> >>>>>
> >>>>>>
> >>>>>> I am not sure what can possibly go wrong in this case. The dssp
> >>>>>> program
> >>>>>> seems to be working (just typing dssp in the shell gives
information
> >>>>>> regarding the versions of dssp that has been used).
> >>>>>>
> >>>>>> The dsspold program doesn't seem to be doing much.
> >>>>>>
> >>>>>>
> >>>>>> No idea what that means, so I can't help with that.
> >>>>>>
> >>>>>
> >>>>> Does anyone know of a version of DSSP executable corresponding
to a
> >>>>>
> >>>>> working
> >>>>>> Gromacs version?
> >>>>>>
> >>>>>>
> >>>>>> DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the
> >>>>>> other
> >>>>>>
> >>>>> day), but in principle any 2.x version should work with GROMACS 4.6
or
> >>>>> newer (the issue was closed 3 years ago, with minimal reported
issues
> >>>>> and
> >>>>> no code modifications since).
> >>>>>
> >>>>> -Justin
> >>>>>
> >>>>>
> >>>>> On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul <jalemkul at vt.edu>
> >>>>> wrote:
> >>>>>
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>> On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:
> >>>>>>>
> >>>>>>> Thanks for your reply. Couple of things.
> >>>>>>>
> >>>>>>> I don't really know where to get older dssp binaries. I couldn't
> >>>>>>>> find
> >>>>>>>> them
> >>>>>>>> available for download in the dssp website.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> http://swift.cmbi.ru.nl/gv/dssp/
> >>>>>>>>
> >>>>>>>>
> >>>>>>> Click on "Distributions" and at the bottom of that page,
"DSSPold" is
> >>>>>>> the
> >>>>>>> old version.
> >>>>>>>
> >>>>>>> I renamed the mkdssp binary to dssp so I am sure nothing is
wrong
> >>>>>>> out
> >>>>>>>
> >>>>>>> there
> >>>>>>>
> >>>>>>>> when I export the binaries for utilization in gromacs.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Aside from the usual advice of making sure the binary is
actually
> >>>>>>>>
> >>>>>>> executable (and actually runs, check with ./dssp -V for instance),
> >>>>>>> there's
> >>>>>>> little to go on here.
> >>>>>>>
> >>>>>>> -Justin
> >>>>>>>
> >>>>>>>
> >>>>>>> On Feb 16, 2015 3:45 PM, "Justin Lemkul" <jalemkul at vt.edu>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>
> >>>>>>>> On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:
> >>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6
and
> >>>>>>>>> there
> >>>>>>>>> is
> >>>>>>>>>
> >>>>>>>>> not
> >>>>>>>>>
> >>>>>>>>>> a scope to specify using the -ver command in this particular
> >>>>>>>>>> version
> >>>>>>>>>> as
> >>>>>>>>>> opposed to the newer versions (5.0.4).
> >>>>>>>>>>
> >>>>>>>>>> By '....' I meant
> >>>>>>>>>>
> >>>>>>>>>> do_dssp -f prot.xtc -s prot.tpr.
> >>>>>>>>>>
> >>>>>>>>>> How do I specify a dssp version in gromacs-4.5.6?
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> I forget when the -ver flag was introduced. Safe bet is if
> >>>>>>>>>> you're
> >>>>>>>>>>
> >>>>>>>>>> using
> >>>>>>>>>>
> >>>>>>>>> an ancient GROMACS version, you need a similarly ancient DSSP
> >>>>>>>>> (version
> >>>>>>>>> 1.0.x).
> >>>>>>>>>
> >>>>>>>>> Secondly, I did install Gromacs-5.0.4 for comparison, and
I am
> >>>>>>>>> using
> >>>>>>>>> DSSP
> >>>>>>>>>
> >>>>>>>>> 2.0.4 again. This time I am using
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> do_dssp -f prot.xtc -s prot.tpr -ver 2
> >>>>>>>>>>
> >>>>>>>>>> The output I am getting is shown below. Not sure what is going
on.
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> *There are 18 residues in your selected groupdssp
> >>>>>>>>>> cmd='/usr/bin/mkdssp
> >>>>>>>>>> -i
> >>>>>>>>>> ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame
> >>>>>>>>>> 0
> >>>>>>>>>> time
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> My guess is that "mkdssp" is not actually the same thing as
> >>>>>>>>>> "dssp" -
> >>>>>>>>>>
> >>>>>>>>>> make
> >>>>>>>>> sure you've installed a real, functional dssp binary.
> >>>>>>>>>
> >>>>>>>>> -Justin
> >>>>>>>>>
> >>>>>>>>> 0.000 Back Off! I just backed up ddJszHtZ to
> >>>>>>>>>
> >>>>>>>>> ./#ddJszHtZ.1#----------------------------------------------
> >>>>>>>>>
> >>>>>>>>> ---------Program
> >>>>>>>>>> do_dssp, VERSION 5.0.4Source code file:
> >>>>>>>>>> /home/apratim/Programs/gromacs-5.0.4/src/gromacs/
> >>>>>>>>>> gmxana/gmx_do_dssp.c,
> >>>>>>>>>>
> >>>>>>>>>> line: 670Fatal error:Failed to execute command: Try specifying
> >>>>>>>>>> your
> >>>>>>>>>> dssp
> >>>>>>>>>> version with the -ver option.For more information and tips for
> >>>>>>>>>> troubleshooting, please check the GROMACSwebsite at
> >>>>>>>>>> http://www.gromacs.org/Documentation/Errors
> >>>>>>>>>> <http://www.gromacs.org/Documentation/Errors>---------
> >>>>>>>>>> ----------------------------------------------*
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>>
> >>>>>>>>>> ==================================================
> >>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Justin A. Lemkul, Ph.D.
> >>>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>>>>>>>
> >>>>>>>>> Department of Pharmaceutical Sciences
> >>>>>>>>> School of Pharmacy
> >>>>>>>>> Health Sciences Facility II, Room 629
> >>>>>>>>> University of Maryland, Baltimore
> >>>>>>>>> 20 Penn St.
> >>>>>>>>> Baltimore, MD 21201
> >>>>>>>>>
> >>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>>>>>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>>>>>>
> >>>>>>>>> ==================================================
> >>>>>>>>> --
> >>>>>>>>> Gromacs Users mailing list
> >>>>>>>>>
> >>>>>>>>> * Please search the archive at http://www.gromacs.org/
> >>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>>>>>>
> >>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>>>>>
> >>>>>>>>> * For (un)subscribe requests visit
> >>>>>>>>>
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >>>>>>>>> or
> >>>>>>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>>> ==================================================
> >>>>>>>>
> >>>>>>>
> >>>>>>> Justin A. Lemkul, Ph.D.
> >>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>>>>>
> >>>>>>> Department of Pharmaceutical Sciences
> >>>>>>> School of Pharmacy
> >>>>>>> Health Sciences Facility II, Room 629
> >>>>>>> University of Maryland, Baltimore
> >>>>>>> 20 Penn St.
> >>>>>>> Baltimore, MD 21201
> >>>>>>>
> >>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>>>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>>>>
> >>>>>>> ==================================================
> >>>>>>> --
> >>>>>>> Gromacs Users mailing list
> >>>>>>>
> >>>>>>> * Please search the archive at http://www.gromacs.org/
> >>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>>>>
> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>>>
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> >>>>>>> or
> >>>>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>> ==================================================
> >>>>>
> >>>>> Justin A. Lemkul, Ph.D.
> >>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>>>
> >>>>> Department of Pharmaceutical Sciences
> >>>>> School of Pharmacy
> >>>>> Health Sciences Facility II, Room 629
> >>>>> University of Maryland, Baltimore
> >>>>> 20 Penn St.
> >>>>> Baltimore, MD 21201
> >>>>>
> >>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>>
> >>>>> ==================================================
> >>>>> --
> >>>>> Gromacs Users mailing list
> >>>>>
> >>>>> * Please search the archive at http://www.gromacs.org/
> >>>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>>
> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>
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or
> >>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>
> >>>>>
> >>>>> --
> >>> ==================================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>
> >>> Department of Pharmaceutical Sciences
> >>> School of Pharmacy
> >>> Health Sciences Facility II, Room 629
> >>> University of Maryland, Baltimore
> >>> 20 Penn St.
> >>> Baltimore, MD 21201
> >>>
> >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>> http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>> ==================================================
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/
> >>> Support/Mailing_Lists/GMX-Users_List before posting!
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> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
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