[gmx-users] Regarding DSSP

HANNIBAL LECTER hanniballecter13 at gmail.com
Tue Feb 17 00:55:57 CET 2015 

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.

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/
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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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>>>>>
>>>>>
>>>>>  --
>>> ==================================================
>>>
>>> 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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>>>
> --
> ==================================================
>
> 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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