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 <jalem...@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 <jalem...@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" <jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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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-requ...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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