[gmx-users] Regarding DSSP
HANNIBAL LECTER
hanniballecter13 at gmail.com
Tue Feb 17 01:13:34 CET 2015
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:
>>>>
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>>>>
>>>>
>>>>
>>>> *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!
>>>>>>>>>
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>>>>>>>>>
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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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>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>
>>>>> 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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>>>
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>>>
>>>
> --
> ==================================================
>
> 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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