Hi ALL,
Is there any way to get the percentage of each secondary structural content
of a protein using do_dssp if I supply a single PDB to it?
And how to plot the data of the -sc output from do_dssp?
Any suggestion is welcome.
Regards,
Anirban
--
gmx-users mailing listgmx-users@gromacs.org
On 11/7/13 8:24 AM, Anirban wrote:
Hi ALL,
Is there any way to get the percentage of each secondary structural content
of a protein using do_dssp if I supply a single PDB to it?
The output of scount.xvg has the percentages, but it's also trivial to do it for
one snapshot. The contents of
On 10/13/13 11:56 PM, Mass wrote:
Hi Justin
Here is the copied and pasted output
Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls
-l
-rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr
Try giving readable permissions to all, i.e. chmod +r.
Hi Justin
Here is the copied and pasted output
Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$
ls -l
total 92332632
-rw-rw-r-- 1 Mass Mass 0 Sep
8 19:46 310Helix.dat
-rw--- 1 Mass Mass 371878 Aug
21 07:39 3BLG_115XrayWater.top
-rw-rw-r-- 1 Mass
Dear users;
I am trying to run DSSP and have problem, I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code file:
On 10/12/13 6:08 PM, Mass wrote:
Dear users;
I am trying to run DSSP and have problem, I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code
On 10/11/13 1:34 AM, Mass wrote:
Dear Mark,
Thanks for your comments, I uninstalled my previous Gromacs version ( from
Ubuntu software centre I just removed it) . and followed the dirty and quick
installation on Gromacs website
tar xfz gromacs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd
Hi Justin,
Sorry for the mistake,
I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line:
On 10/11/13 8:12 AM, Mass wrote:
Hi Justin,
Sorry for the mistake,
I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code file:
Dear Gromacs user,
Can anyone tell me how to arrange for my login scripts to source gromacs
automatically? Justin just point that to me and in Gromacs website it is
written search the web for that, anyone know how to do that?
Thanks
On Saturday, October 12, 2013 1:12 AM, Mass
On 10/11/13 8:57 AM, Mass wrote:
Dear Gromacs user,
Can anyone tell me how to arrange for my login scripts to source gromacs
automatically? Justin just point that to me and in Gromacs website it is written
search the web for that, anyone know how to do that?
It depends on your shell. In
Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue.
Google knows a lot more about it than anybody here ;-)
Mark
On Fri, Oct 11, 2013 at 2:57 PM, Mass masstransfer_2...@yahoo.com wrote:
Dear Gromacs user,
Can anyone tell me how to arrange for my login scripts to source
Dear Gromacs users,
I have asked this questions before and Justin gave some answers which I could
solve my problem based on his answer. I am using Ubuntu 12.10 and installed
gromacs 4.5.5-2.
this is what I have done
2- I moved this file to usr/local/bin
1- first I downloaded the dssp
wget
Hi,
Since the release of 4.5.5, DSSP totally changed its command-line
interface. So old GROMACS code cannot work with new DSSP. You need to get
the old version of DSSP to use with old GROMACS, or new GROMACS code to
work with either DSSP.
Mark
On Thu, Oct 10, 2013 at 1:37 PM, Mass
Dear Mark,
Thanks for your comments, I uninstalled my previous Gromacs version ( from
Ubuntu software centre I just removed it) . and followed the dirty and quick
installation on Gromacs website
tar xfz gromacs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
Dear all,
I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp command but get the following error each
time:
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68
/dev/null 2 /dev/null
Is there any way to rectify
Hi,
Search the mailing list. This problem and its solution has been repeatedly
discussed.
Erik
On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Dear all,
I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp
Yes I did searched. But for most people, there were issues regarding the
path or wrong DSSP.
DSSP runs for me, but do_dssp does not.
On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
Search the mailing list. This problem and its solution has been repeatedly
Right. And what is its location?
On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:
Yes I did searched. But for most people, there were issues regarding the
path or wrong DSSP.
DSSP runs for me, but do_dssp does not.
On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund
The location of dssp is /usr/local/bin/dssp
On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Right. And what is its location?
On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:
Yes I did searched. But for most people, there were issues
Search again. The syntax for invoking dssp changed at some point and it took a
while before do_dssp adapted to that. If your do_dssp is lacking the -ver
option then I'm quite confident that it uses the old syntax, which doesn't work
with the newer versions (v. 2.0+ I think) of dssp.
Erik
On
Yes I checked. do_dssp has no -ver option.
I also found out this link
https://gerrit.gromacs.org/#/c/687/
but dont know how to install/use it.
Or maybe I can install DsspOld and see?
On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Search again. The syntax for
You have (at least) two easy options.
1) Install old_dssp that is available through the dssp web page.
2) Install a newer version of gromacs than you have at the moment. What version
do you currently use?
Erik
On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Yes
My current Gromacs version is 4.5.5
I think using the first option will be easy and quick.
On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
You have (at least) two easy options.
1) Install old_dssp that is available through the dssp web page.
2) Install a newer
Hi Rama,
I bet that wasn't the only output you got. Two things can usually
happen with do_dssp. Either you chose the wrong group for analysis, or
there is a problem with the version of DSSP. Probably the latter: DSSP
syntax changed recently, and I think that GMX 4.5.5 can't deal with
that. There
Hi all,
I downloaded the original form of DSSP which is recently called
DSSPold. Whenever I use the following:
*do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm *
It selects Protein by it-self without any control from me. I want to
choose from the list, for example not protein but C-alpha.
To
On 6/7/12 10:07 AM, Turgay Cakmak wrote:
Hi all,
I downloaded the original form of DSSP which is recently called
DSSPold. Whenever I use the following:
*do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm *
It selects Protein by it-self without any control from me. I want to choose
from the
Hi Justin,
Thank you for your descriptive reply.
I prepared new index.file which includes mainchain, and when I used the
do_dssp with -n index.ndx, it worked.
But, if I doesn't use the index file, again, the Protein is selected by
the system. It is weird..
Best regards,
Deniz
On Thu, Jun 7,
Dear all,
How to install DSSP in Gromacs 4.5.5.
i set environmental variable export DSSP=/usr/local/bin/dssp and checked.
I have refereed many posts related to dssp issue and tried with new and old
dssp executable but confused.
While running i got error Segmentation fault.
Help me to solve
On 16/05/2012 4:54 PM, Sathish wrote:
Dear all,
How to install DSSP in Gromacs 4.5.5.
i set environmental variable export DSSP=/usr/local/bin/dssp and
checked.
I have refereed many posts related to dssp issue and tried with new
and old dssp executable but confused.
While running i got
Dear Sir,
Thank u for reply and the old dssp executable was working fine,
[root@localhost]# dssp
COPYRIGHT
W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
CMBI version by elmar.krie...@cmbi.ru.nl / April 1, 2010
USAGE
dssp [Options] PDB_File DSSP_File - Read PDB_File
On 16/05/2012 5:33 PM, Sathish wrote:
Dear Sir,
Thank u for reply and the old dssp executable was working fine,
[root@localhost]# dssp
COPYRIGHT
W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
CMBI version by elmar.krie...@cmbi.ru.nl
mailto:elmar.krie...@cmbi.ru.nl
Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
get the dssp plot.
Thanks
bunty
--
On 14/05/2012 4:14 PM, bunty xy wrote:
Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
Dear ALL:how to install DSSP in Gromacs4.5.7I followed someone replies mail
still can not use do I do right ?DSSP
website-miscellaneous-distribution-dsspold-linux distribution then get
dsspcmbibut Gromacs can not recoginz this index gromacs index is do_dssp ?and
DSSPagain , how to install
You set the environment variable DSSP to the absolute path to your dssp
executable. Then do_sddp can make use of it. Is that clear?
Erik
26 apr 2012 kl. 09.33 skrev 李 麗花:
Dear ALL:
how to install DSSP in Gromacs4.5.7
I followed someone replies mail still can not use
do I do right ?
DSSP
hello:
I am trying to run do_dssp by command:
do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm
but it said:
Select a group: 1
Selected 1: 'Protein'
There are 35 residues in your selected group
trn version: GMX_trn_file (single precision)
Reading frame 400 time 400.000
Back Off! I
What's your dssp version? The most recent ones have different flags that are
not yet supported by gromacs.
Erik
27 mar 2012 kl. 11.50 skrev Albert:
hello:
I am trying to run do_dssp by command:
do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm
but it said:
Select a group: 1
Hi,
I used to have similar problem. Try using double precision. Worked for me.
Best
Quoting Albert mailmd2...@gmail.com:
hello:
I am trying to run do_dssp by command:
do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm
but it said:
Select a group: 1
Selected 1: 'Protein'
There are 35
On 27/03/2012 8:50 PM, Albert wrote:
hello:
I am trying to run do_dssp by command:
do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm
but it said:
Select a group: 1
Selected 1: 'Protein'
There are 35 residues in your selected group
trn version: GMX_trn_file (single precision)
Reading
On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 2/03/2012 6:52 PM, lina wrote:
Hi,
is the old dssp not compatible with the gromacs 4.5.5 ?
I am confused,
Thanks,
Best regards,
The new DSSP is not compatible with any GROMACS
Ha ... the dssp complain the
Gromacs' 4.5.5 do_dssp is broken. There is a patch for it in git. I haven't
tried it out, so I can't say for sure it works. This is not a DSSP problem,
it's a Gromacs problem. Just to reinforce the idea, the new DSSP should not
be used, no matter which Gromacs version you're using.
Best regards,
Hi,
is the old dssp not compatible with the gromacs 4.5.5 ?
I am confused,
Thanks,
Best regards,
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
On 2/03/2012 6:52 PM, lina wrote:
Hi,
is the old dssp not compatible with the gromacs 4.5.5 ?
I am confused,
Thanks,
Best regards,
The new DSSP is not compatible with any GROMACS
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
On 25/12/2010 11:03 PM, mustafa bilsel wrote:
Hi Justin,
maybe I am making a mistake with installation. What I am doing is this:
I am creating a diretory called DSSP, then I write
rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ http://rsync.cmbi.ru.nl/dssp/
/home/m/DSSP/
on the terminal, and then
http://biskit.pasteur.fr/install/applications/dssp
wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip
unzip dsspcmbi.zip
cd dssp
./DsspCompileGCC
cd ..
sudo mv dssp /usr/local/src/
cd /usr/local/bin
sudo ln -s ../src/dssp/dsspcmbi .
lina
On Sat, Dec 25, 2010 at 8:45 PM, Mark
mustafa bilsel wrote:
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv DSSP /path/to/dssp
On Fri, Dec 24, 2010 at 11:38 AM, mustafa bilsel mfbil...@gmail.com wrote:
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv DSSP /path/to/dssp
Hi,
I installed in /usr/local/bin the DSSP program. And I set the environment
variable with a command such as “export DSSP=/usr/local/bin/dssp”.
a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc
...
Selected 1: 'Protein'
There are 164 residues in your selected group
Opening library file
...@gromacs.org] on behalf
of ahmet yıldırım [ahmedo...@gmail.com]
Sent: Wednesday, November 10, 2010 10:02 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] DSSP error
Hi,
I installed in /usr/local/bin the DSSP program. And I set the environment
variable with a command such as “export
--
*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of ahmet yıldırım [ahmedo...@gmail.com]
*Sent:* Wednesday, November 10, 2010 10:02 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] DSSP error
Hi,
I installed in /usr/local
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] DSSP error
Hi,
I installed in /usr/local/bin the DSSP program. And I set the
environment variable with a command such as “export
DSSP=/usr/local/bin/dssp”.
a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] DSSP error
Hi,
I installed in /usr/local/bin the DSSP program. And I set the
environment variable with a command such as “export
DSSP=/usr/local/bin/dssp
mailto:ahmedo...@gmail.com
mailto:ahmedo...@gmail.com mailto:ahmedo...@gmail.com]
*Sent:* Wednesday, November 10, 2010 10:02 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] DSSP error
Hi,
I installed in /usr/local/bin
*Subject:* [gmx-users] DSSP error
Hi,
I installed in /usr/local/bin the DSSP program. And I
set the
environment variable with a command such as “export
DSSP=/usr/local/bin/dssp”.
a...@ubuntu:/Desktop/work
mailto:ahmedo...@gmail.com]
*Sent:* Wednesday, November 10, 2010 10:02 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] DSSP error
Hi,
I installed in /usr/local/bin the DSSP program. And I
May be the directory you are working in is read only, as Justin mentioned
this could be a permissions issue.
As an example the super computer that I use, cannot write anything in the
home directory, therefore all simulations and analysis are done in scratch.
Ali
--
gmx-users mailing list
1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz
2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC
3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp
4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export
DSSP=/usr/local/bin/dssp
Dear Justin,
I compiled the
ahmet yıldırım wrote:
1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz
2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC
3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp
4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export
DSSP=/usr/local/bin/dssp
Dear Justin,
Finally, The problem is solved, Thank you very much for your patience.
Ps: I set *r...@ab-desktop:/home/ab/Desktop/dssp# export
DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run
again.The I don't still understand why the DSSP environment variable is not
run.
ahmet yıldırım wrote:
Dear Justin,
Finally, The problem is solved, Thank you very much for your patience.
Ps: I set *r...@ab-desktop:/home/ab/Desktop/dssp# export
DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run
again.The I don't still understand why the DSSP
I do not have any problem. The problem is solved.
Thank you very much
10 Kasım 2010 22:45 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı:
ahmet yıldırım wrote:
Dear Justin,
Finally, The problem is solved, Thank you very much for your patience.
Ps: I set
Hi,
Program do_dssp, VERSION 4.0.7
Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471
Fatal error:
Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2
/dev/null
It came out two or three file like ddEPI6I2 and then died like above.
My first time
#ZHAO LINA# wrote:
Hi,
Program do_dssp, VERSION 4.0.7
Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471
Fatal error:
Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null
2 /dev/null
It came out two or three file like ddEPI6I2 and then died
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
#ZHAO LINA# wrote:
Hi,
Program
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
#ZHAO LINA# wrote:
Hi,
Program do_dssp, VERSION 4.0.7
: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
#ZHAO LINA# wrote:
Hi,
Program do_dssp, VERSION 4.0.7
Source code file
, November 05, 2010 9:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
What did you try to do? To use dssp, you must select entire residues,
e.g. 1 (protein). That error sounds a bit like my problem when trying
to do dssp using only the backbone.
// Linus Östberg
On Fri, Nov 5
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
Linus Östberg wrote:
What did
...@e.ntu.edu.sg]
Sent: Friday, November 05, 2010 9:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] dssp
Hi,
1. There is no wrong in mine executable path, it's mine fault that I MODIFIED
the real and true path to a simple way as it showed pathTo... before I
posted.
2. seems
...@e.ntu.edu.sg]
Sent: Friday, November 05, 2010 9:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] dssp
Hi,
1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and
true path to a simple way as it showed pathTo... before I posted.
2. seems
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
#ZHAO LINA# wrote:
But right now I noticed something a bit funny,
Try different times,
Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
#ZHAO LINA# wrote:
But right now
Which among DSSP and g_sas is better for calculating solvent accessible
surface area of proteins?
--
Bhanu Prakash.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Bhanu Prakash Sandaka wrote:
Using DSSP we can also calcuate the surface area, though it doesn't allow
changes in probe diameter etc. it does calculate the surface area. I just
wish to know whether the performance of DSSP is comparable to g_sas?
Should it be used?
From do_dssp -h:
Note that
Hi Shahid,
I have fixed the problem in do_dssp. You can either pull the
newest release-4-0-patches branch from the git repository
or change ./src/tools/do_dssp.c, line 80 from
snew(ssbuf,nres+10);
to:
snew(ssbuf, 2*nres-1);
Carsten
On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote:
Hi,
there was a problem in do_dssp when used on proteins with more
than 10 chains. Is this the case? I just saw that I
only fixed that in the head, but not in 4.0.x.
Carsten
On May 18, 2010, at 3:49 PM, shahid nayeem wrote:
Hi
When I run dssp alone with a .pdb file it works well. But
Dear All
I downloaded dsspcmbi.tar.gz, and compiled using command
./DsspCompileGCC as given in Readme.txt file. when I try to run
do_dssp command in gromacs I get error
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
I checked for DSSP executible in
shahid nayeem wrote:
Dear All
I downloaded dsspcmbi.tar.gz, and compiled using command
./DsspCompileGCC as given in Readme.txt file. when I try to run
do_dssp command in gromacs I get error
Well, what happened?
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv
Hi
After posting this mail I did some google search and after changing the
executible name to dssp I moved it in /usr/local/bin/ After this when I did
do_dssp it starts running asks to select a group I choose main chain 5, then
it generates some intermediate file and gives error as segmentation
shahid nayeem wrote:
Hi
After posting this mail I did some google search and after changing the
executible name to dssp I moved it in /usr/local/bin/ After this when I
did do_dssp it starts running asks to select a group I choose main chain
5, then it generates some intermediate file and
-users-boun...@gromacs.org]on
Behalf Of shahid nayeem
Sent: Tuesday, May 18, 2010 5:17 PM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] DSSP
Hi
After posting this mail I did some google search and after changing the
executible name to dssp I moved it in /usr/local
Hi
When I run dssp alone with a .pdb file it works well. But when I run with
Gromacs as do_dssp it gives segmentation fault and does not do any
calculation except giving some intermediate files as follows.
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
Reading frame 0
shahid nayeem wrote:
Hi
When I run dssp alone with a .pdb file it works well. But when I run
with Gromacs as do_dssp it gives segmentation fault and does not do any
calculation except giving some intermediate files as follows.
Opening library file
pawan raghav wrote:
I have download dsspcmbi.zip and extract the dssp folder into
/cygdrive/c/cygwin/usr/local/bin/ directory. Then
set the environment variable export
DSSP=/cygdrive/c/cygwin/usr/local/bin/dssp for bash. then I have gone to
my folder by using cd where all my md files were
vivek modi wrote:
hi,
Although this is already discussed in the mailing list but none of the
solutions mentioned helped me.
I am using Gromacs-4.0.5. I downloaded dssp
from http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
Then I copy this to /usr/local/bin chmod to executable.
But when I
On 2010-04-04 06.40, Chih-Ying Lin wrote:
HI
1. dssp -n index.ndx
= only atom numbers of one residue in the index.ndx
= can dssp decide the exact second structure for the only one residue
without considering other residues of protein?
no.
= can i get the same second structure for the
Hi
With the following two commands,
do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg
xpm2ps -f secondary-structure.xpm -o secondary-structure.eps
With GIMP, i can see the secondary structure plot. The legend indicates the
color of different second
Chih-Ying Lin wrote:
Hi
With the following two commands,
do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg
xpm2ps -f secondary-structure.xpm -o secondary-structure.eps
With GIMP, i can see the secondary structure plot. The legend indicates
HI
How to pass an .m2p file to xpm2ps to change the dimensions
of the plot, data point size, etc. ???
Thank you
Lin
Chih-Ying Lin wrote:
Hi
With the following two commands,
do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg
xpm2ps -f
Chih-Ying Lin wrote:
HI
How to pass an .m2p file to xpm2ps to change the dimensions
of the plot, data point size, etc. ???
Use the -di flag of xpm2ps.
http://manual.gromacs.org/current/online/m2p.html
-Justin
Thank you
Lin
Chih-Ying Lin wrote:
Hi
With the following two
Chih-Ying Lin wrote:
HI
After running DSSP, .eps files are created.
No they aren't; you create .eps files from the .xpm output that do_dssp
generates.
We can see the second structures of the all residues.
I only want to see the change of the second structures of some specific
On 4/3/10 9:19 PM, Justin A. Lemkul wrote:
Chih-Ying Lin wrote:
HI After running DSSP, .eps files are created.
No they aren't; you create .eps files from the .xpm output that do_dssp
generates.
We can see the second structures of the all residues.
I only want to see the change of the
HI
1. dssp -n index.ndx
= only atom numbers of one residue in the index.ndx
= can dssp decide the exact second structure for the only one residue
without considering other residues of protein?
= can i get the same second structure for the residue with [ dssp -n
one-residue.ndx ] and [dssp -n
Hello
I installed the dssp program for obtaining the secondary structure.I used the
dssp programm to analyze the secondary structure of the protein after a MD
simulation run. I got the out of the pogramm as m.dssp but I want to know how
do I represent the output of the dssp programm graphically
subarna thakur wrote:
Hello
I installed the dssp program for obtaining the secondary structure.I
used the dssp programm to analyze the secondary structure of the protein
after a MD simulation run. I got the out of the pogramm as m.dssp but I
want to know how do I represent the output of the
Dear all,
I wanted to get the dssp output of Coarse Grained structure of my protein
i.e. 1K4C. In order to get that I have a script which is given to me in the
MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully
in my linux machine. In my first step i cleaned the 1K4C
sunny mishra wrote:
Dear all,
I wanted to get the dssp output of Coarse Grained structure of my
protein i.e. 1K4C. In order to get that I have a script which is given
to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the
dssp successfully in my linux machine. In my first
1 - 100 of 118 matches
Mail list logo
