On 12/16/19 12:21 PM, Iman Katouzian wrote:
Good day,
I am using do_dssp to determine the secondary structure of my protein
however when I run my code :
gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg
-tu ns
I encounter this, and after several minutes the reading time
Good day,
I am using do_dssp to determine the secondary structure of my protein
however when I run my code :
gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg
-tu ns
I encounter this, and after several minutes the reading time frames is
still ZERO!!
I have already did chmod
hi mark,
i'm using gromacs 4.65 and dssp version is 2.04.
Where i can download a older dssp version ?
thank you
On Mon, Sep 12, 2016 at 9:52 PM, Mark Abraham
wrote:
> Hi,
>
> Then like Justin said, dssp must be of a version unsuitable for do_dssp,
> e.g. you're using an ancient GROMACS do_dss
Hi,
Then like Justin said, dssp must be of a version unsuitable for do_dssp,
e.g. you're using an ancient GROMACS do_dssp and a new version of dssp.
Mark
On Mon, Sep 12, 2016 at 5:15 PM Samith Rathnayake
wrote:
> located on /usr/local/bin/dssp . thus in my .bashrc i do not set the DSSP
> envir
located on /usr/local/bin/dssp . thus in my .bashrc i do not set the DSSP
environment.
On Mon, Sep 12, 2016 at 9:29 PM, Justin Lemkul wrote:
>
>
> On 9/12/16 11:56 AM, Samith Rathnayake wrote:
>
>> and now this is what i got when do_dssp run : Fatal error:
>> DSSP executable (/usr/local/bin/dssp
On 9/12/16 11:56 AM, Samith Rathnayake wrote:
and now this is what i got when do_dssp run : Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
but dssp binary (NOT do_dssp) directly on a PDB file is working
This is what I meant in point 2. $DSSP needs to po
and now this is what i got when do_dssp run : Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
but dssp binary (NOT do_dssp) directly on a PDB file is working
On Mon, Sep 12, 2016 at 9:21 PM, Samith Rathnayake
wrote:
> 1/ yes it working on pdb
> 3/dssp-2.04
>
1/ yes it working on pdb
3/dssp-2.04
thank you
On Mon, Sep 12, 2016 at 8:39 PM, Justin Lemkul wrote:
>
>
> On 9/12/16 11:06 AM, Samith Rathnayake wrote:
>
>> thank you
>>
>> I really appreciate if anyone can tell me simple and step-by step
>> solution
>>
>>
> There are many things that could be
On 9/12/16 11:06 AM, Samith Rathnayake wrote:
thank you
I really appreciate if anyone can tell me simple and step-by step
solution
There are many things that could be wrong. Most of the normal troubleshooting
can be found with a simple Google search (that's why we have an archive!) but I
thank you
I really appreciate if anyone can tell me simple and step-by step
solution
thank you
regards
samith
On Mon, Sep 12, 2016 at 7:09 PM, Sarath Chandra <
sarathchandrada...@gmail.com> wrote:
> dssp by default gets installed as mkdssp.
>
> Do an export DSSP=path_to_mkdssp_executable
>
dssp by default gets installed as mkdssp.
Do an export DSSP=path_to_mkdssp_executable
and it will worl
On 12 September 2016 at 18:01, Samith Rathnayake
wrote:
> Dear all
>
> When i'm run the do_dssp command in the gromacs
>
> do_dssp -f ../run01/run01.trr -s ../run01/run01.tpr -sc scount.xvg -
Dear all
When i'm run the do_dssp command in the gromacs
do_dssp -f ../run01/run01.trr -s ../run01/run01.tpr -sc scount.xvg -o
ss.xpm -dt 10 -ver 2
i got this error
There are 455 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd5J9xcr -o ddPd7b8G > /dev/null 2>
/dev/null'
trn
On 5/4/16 9:20 AM, Chalaoux, Francois-Regis wrote:
Hi everybody,
Trying to use do_dssp_mpi for my MD I got an error described below.
I gave "-ver 2" for dssp 2.0.4 but nothing changed.
This is a real pain in the neck since a week to debug this message.
Any tracks Guys ?
The usual tips are
Hi everybody,
Trying to use do_dssp_mpi for my MD I got an error described below.
I gave "-ver 2" for dssp 2.0.4 but nothing changed.
This is a real pain in the neck since a week to debug this message.
Any tracks Guys ?
FRC
Config:
Linux Centos 6.7
Gromacs mpi 5.04
==
CMD and Erro
Dear Khatnaa,
I would certainly downsample using -dt. Unless, of course, you really need to
know the secondary structure over 30 frames. That said, I think do_dssp
should be able to handle large trajectories, so this might be a bug in some
sense.
Kind regards,
Erik
> On 22 Mar 2016, at 16
Dear Gmx-Users,
I had done roughly 300ns peptide and membrane simulation. I am trying to do
some analyses through the do_dssp. To get in .xpm file I put .xtc and .tpr
files. Then at certain frame its just killed and gave me the empty files with
strange names like ddccTf1j, ddmMD9pt, ddmuWFKI
Thanks Mark.
On Fri, May 22, 2015 at 3:17 PM, Mark Abraham
wrote:
> Yes
>
> On Fri, May 22, 2015 at 2:59 PM MUSYOKA THOMMAS <
> mutemibiochemis...@gmail.com> wrote:
>
> > Hi Gromacs users,
> > I did my simulations using an older version of GROMACS (ie 4.5.7) and
> after
> > reading through vario
Yes
On Fri, May 22, 2015 at 2:59 PM MUSYOKA THOMMAS <
mutemibiochemis...@gmail.com> wrote:
> Hi Gromacs users,
> I did my simulations using an older version of GROMACS (ie 4.5.7) and after
> reading through various posts, it seems I have to do the dssp analysis
> using a newer version. Can I use
Hi Gromacs users,
I did my simulations using an older version of GROMACS (ie 4.5.7) and after
reading through various posts, it seems I have to do the dssp analysis
using a newer version. Can I use the trajectories I got from the previous
older version of GROMACS to perform dssp analysis on Gromacs
Hi Tsjerk,
Thank you for the reply.
The coarse graining was done using MARTINI according to tutorials mentioned in
their website.
Best, Sandhyaa
On Tuesday, 21 April 2015 12:46 PM, Tsjerk Wassenaar
wrote:
Hi Sandhyaa,
DSSP doesn't work on C-alpha only or coarse-grained trajecto
Hi Sandhyaa,
DSSP doesn't work on C-alpha only or coarse-grained trajectories. Can you
maybe specify what coarse-grain FF you're using? It may be possible to use
the tool 'backward' to convert it to atomistic.
Cheers,
Tsjerk
On Tue, Apr 21, 2015 at 6:48 AM, Sandhyaa Subramanian wrote:
> Dear
Dear All,
I have a trajectory with the protein represented by C-Alpha atoms only. I was
wondering if I could use ' do_dssp ' for predicting the secondary structure for
this trajectory. When I tried to do so ( do_dssp -f trajca.xtc -s reference.pdb
-o dssp_traj ) I got the following error -
F
Dear Mahboobeh,
did you try to specify your version? Maybe -ver 1.0 works.
Good luck!
Best,
Marianne
On 10.10.14 09:39, Mahboobeh Eslami wrote:
>
> hi dear justini use gromacs4.6.5 for protein-ligand complex simulationi wasn
> to study second structure of my protein for 20ns simulation. i u
dera mariannethanks for your replyI did not find version 1.0. i found only
DSSPold of http://swift.cmbi.ru.nl/gv/dssp/)
Thank you sincerely for your help
On Friday, October 10, 2014 11:19 AM, Marianne Schulte
wrote:
Dear Mahboobeh,
did you try to specify your version? Maybe -ver
hi dear justini use gromacs4.6.5 for protein-ligand complex simulationi wasn
to study second structure of my protein for 20ns simulation. i used DSSP . I
copied dssp file in /local/usr/bin and use following commandschmod +x
dssp./dsspwhen i use following command:do_dssp -f md.xtc -s md.tpr -o
hi GMX usersi use gromacs4.6.5 for protein-ligand complex simulationi wasn to
study second structure of my protein for 20ns simulation. i used DSSP . I
copied dssp file in /local/usr/bin and use following commandschmod +x
dssp./dsspwhen i use following command:do_dssp -f md.xtc -s md.tpr -o
m
On 8/17/14, 12:41 AM, Batdorj Batsaikhan wrote:
Thank you Justin,
It is working but how can I adjust x-axis. My figure y-axis is ok, and x-axis
has not time.
You'll need to post your .m2p file and a link to an image of the output. None
of the settings should be able to remove an axis lab
Thank you Justin,
It is working but how can I adjust x-axis. My figure y-axis is ok, and x-axis
has not time.
Best regards,
Batsaikhan
On Saturday, August 16, 2014 10:00 PM, Justin Lemkul wrote:
On 8/16/14, 7:30 AM, Batdorj Batsaikhan wrote:
> Dear gmx users,
>
> I done secondary st
On 8/16/14, 7:30 AM, Batdorj Batsaikhan wrote:
Dear gmx users,
I done secondary structure analysis using do_dssp. then I converted xpm file to
eps. following commands:
$ gmx do_dssp -s md3.tpr -f md.xtc -o ss.xpm -tu ns -sss -xvg
$ xpm2ps -f ss.xpm -o ss.eps
but result of ss.eps is written
Dear gmx users,
I done secondary structure analysis using do_dssp. then I converted xpm file to
eps. following commands:
$ gmx do_dssp -s md3.tpr -f md.xtc -o ss.xpm -tu ns -sss -xvg
$ xpm2ps -f ss.xpm -o ss.eps
but result of ss.eps is written on the one line. How to fix it?
when I open ss.e
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