[gmx-users] Regarding DSSP
HANNIBAL LECTER
hanniballecter13 at gmail.com
Tue Feb 17 00:40:17 CET 2015
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?
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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>>>>> 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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