[gmx-users] Regarding DSSP
Justin Lemkul
jalemkul at vt.edu
Tue Feb 17 01:06:52 CET 2015
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
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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
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>>>>>> * 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
>>>>
>>>> ==================================================
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>>>> Gromacs Users mailing list
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>>>> * Please search the archive at http://www.gromacs.org/
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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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>>
--
==================================================
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
==================================================
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