[gmx-users] DSSP

[Nikolaos Michelarakis]

Hello,

I am trying to do a secondary structure analysis to get the percentages of
each secondary structure in my protein. I know i can use do_dssp but
unfortunately DSSP is not installed on the cluster that i have been using
and i do not have the acess to install it. Any other ways to do it? or
would anyone be able to run it for me? I need it for 3 structures, for 3
different forcefields, 9 structures overall.

Thanks a lot,

Nicholas
-- 
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.

[gmx-users] DSSP

[Nikolaos Michelarakis]

Hello,

Thank you all for your help! I got it working by downloading the
executables directly and setting the path but i do get the

Program do_dssp, VERSION 5.0
Source code file:
/home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c,
line: 670

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.

error. No matter which version i specify, it persists, any ideas?

Cheers,

Nicholas
-- 
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.

[gmx-users] DSSP

[Sanket Ghawali]

Dear all,
How do i install DSSP for gromacs 5.1.1
I am curently working on Centos
Which version should i download and any commands to install dssp

Thanks & Regards
Sanket
-- 
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.

[gmx-users] DSSP

[Aishwarya Dhar]

Following procedure I have used
1. Downloaded  http://swift.cmbi.ru.nl/gv/dssp/
dssp-2.0.4-linux-i386 and renamed it dssp

2.made dssp  executable  and moved it to usr/local/bin

3.Then ran the command from the current location where the tpr and trr
files are present do_dssp -s  md.tpr -f md.trr -o ss.xpm  -ver 2.0

4.There are 91 residues in your selected group dssp cmd='/usr/local/bin/dssp
-i ddixopnV -o dd4YitS9 > /dev/null 2> /dev/null'
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Back Off! I just backed up ddixopnV to ./#ddixopnV.1#

It seems that the run is going on for two weeks and dssp analysis couldnt
be done
















Thanks




Sincerely

Aishwarya Dhar
-- 
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.

[gmx-users] DSSP

[Mariusz Wierzbowski]

Hi,

I would like to analyze secondary structure elements for my protein. I want 
to do it with do_dssp command in gromacs. I am using gromacs on a plgrid 
platform. The problem is that an error occurs:


Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv 
DSSP).


On other forums I have read about setting the environment with setenv or 
export DSSP

but I think that these solutions are for programs on local system.

I would appreciate any help. Thanks.

Best regards

Mariusz

--
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.

[gmx-users] DSSP

[Vidya R]

Hi gromacs users,

I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)

I want to download and install dssp tool.

How to proceed?


Thanks,
Vidya.R
-- 
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.

[gmx-users] dssp

[Uma Devi]

dear sir/madam
i am new to gromacs. i am trying to install DSSP,i am having centos. i
downloaded the DSSP and pasted it in /usr/local/bin directory
while i am running it shows the following error


Failed to execute command: /usr/local/bin/dssp.exe -na ddLV8RKo ddvXmynp >
/dev/null 2> /dev/null

please help me to get the solutions.
thanks in advance

uma
-- 
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.

Re: [gmx-users] DSSP

[bipin singh]

You may use the precompiled dssp executables.




*Thanks and Regards,Bipin Singh*



On Mon, Aug 25, 2014 at 5:31 AM, Nikolaos Michelarakis 
wrote:

> Hello,
>
> I am trying to do a secondary structure analysis to get the percentages of
> each secondary structure in my protein. I know i can use do_dssp but
> unfortunately DSSP is not installed on the cluster that i have been using
> and i do not have the acess to install it. Any other ways to do it? or
> would anyone be able to run it for me? I need it for 3 structures, for 3
> different forcefields, 9 structures overall.
>
> Thanks a lot,
>
> Nicholas
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Nikolaos Michelarakis]

Hi,

Thank you for your answer, could you please give me some more info on where
to find them and how to use them for the whole trajectory?

Cheers,

Nicholas
-- 
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.

Re: [gmx-users] DSSP

[bipin singh]

You may download the relevant executables from the following links:

ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64
ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386
ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-win32.exe

before using the do_dssp module of Gromacs, export the path to the above
executable dssp as:


export dssp=/path/to/dssp/executable


then run the do_dssp as usual.





*Thanks and Regards,Bipin Singh*




On Mon, Aug 25, 2014 at 7:38 AM, Nikolaos Michelarakis 
wrote:

> Hi,
>
> Thank you for your answer, could you please give me some more info on where
> to find them and how to use them for the whole trajectory?
>
> Cheers,
>
> Nicholas
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Mark Abraham]

You could ask for it to be installed?

Mark


On Mon, Aug 25, 2014 at 2:01 AM, Nikolaos Michelarakis 
wrote:

> Hello,
>
> I am trying to do a secondary structure analysis to get the percentages of
> each secondary structure in my protein. I know i can use do_dssp but
> unfortunately DSSP is not installed on the cluster that i have been using
> and i do not have the acess to install it. Any other ways to do it? or
> would anyone be able to run it for me? I need it for 3 structures, for 3
> different forcefields, 9 structures overall.
>
> Thanks a lot,
>
> Nicholas
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[rama david]

Dear friend,
 I think the VMD can do it.
 Use vmd > extension > analysis > timeline .

It will give the residue with color distinguishing  which are in sec state
with timeframe.
But I dont know will it help in finding the percentage of sec. structure.
Try it and if u find it how to do, post it here so I will also know.


With best regards,
Rama david




On Mon, Aug 25, 2014 at 11:42 AM, Mark Abraham 
wrote:

> You could ask for it to be installed?
>
> Mark
>
>
> On Mon, Aug 25, 2014 at 2:01 AM, Nikolaos Michelarakis 
> wrote:
>
> > Hello,
> >
> > I am trying to do a secondary structure analysis to get the percentages
> of
> > each secondary structure in my protein. I know i can use do_dssp but
> > unfortunately DSSP is not installed on the cluster that i have been using
> > and i do not have the acess to install it. Any other ways to do it? or
> > would anyone be able to run it for me? I need it for 3 structures, for 3
> > different forcefields, 9 structures overall.
> >
> > Thanks a lot,
> >
> > Nicholas
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Mark Abraham]

Have you read and followed gmx do_dssp -h?

Mark


On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis 
wrote:

> Hello,
>
> Thank you all for your help! I got it working by downloading the
> executables directly and setting the path but i do get the
>
> Program do_dssp, VERSION 5.0
> Source code file:
>
> /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c,
> line: 670
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option.
>
> error. No matter which version i specify, it persists, any ideas?
>
> Cheers,
>
> Nicholas
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Nikolaos Michelarakis]

Yes, this is the command i am using:

do_dssp -s npt-nopr.tpr -f npt-nopr.trr -o fws-ss.xpm -ver 2

whether i include -ver 2 or not makes no difference, I still get the same
error.

Cheers,

Nicholas


On 25 August 2014 15:53, Mark Abraham  wrote:

> Have you read and followed gmx do_dssp -h?
>
> Mark
>
>
> On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis 
> wrote:
>
> > Hello,
> >
> > Thank you all for your help! I got it working by downloading the
> > executables directly and setting the path but i do get the
> >
> > Program do_dssp, VERSION 5.0
> > Source code file:
> >
> >
> /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c,
> > line: 670
> >
> > Fatal error:
> > Failed to execute command: Try specifying your dssp version with the -ver
> > option.
> >
> > error. No matter which version i specify, it persists, any ideas?
> >
> > Cheers,
> >
> > Nicholas
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[bipin singh]

check the permissions of dssp executables and give the execute permission
if it is not already.



*Thanks and Regards,Bipin Singh*


On Mon, Aug 25, 2014 at 6:26 PM, Nikolaos Michelarakis 
wrote:

> Yes, this is the command i am using:
>
> do_dssp -s npt-nopr.tpr -f npt-nopr.trr -o fws-ss.xpm -ver 2
>
> whether i include -ver 2 or not makes no difference, I still get the same
> error.
>
> Cheers,
>
> Nicholas
>
>
> On 25 August 2014 15:53, Mark Abraham  wrote:
>
> > Have you read and followed gmx do_dssp -h?
> >
> > Mark
> >
> >
> > On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis  >
> > wrote:
> >
> > > Hello,
> > >
> > > Thank you all for your help! I got it working by downloading the
> > > executables directly and setting the path but i do get the
> > >
> > > Program do_dssp, VERSION 5.0
> > > Source code file:
> > >
> > >
> >
> /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c,
> > > line: 670
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option.
> > >
> > > error. No matter which version i specify, it persists, any ideas?
> > >
> > > Cheers,
> > >
> > > Nicholas
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Mark Abraham]

Hi,

gmx do_dssp -h has some useful instructions.

Mark

On Thu, Jul 7, 2016 at 9:04 AM Sanket Ghawali 
wrote:

> Dear all,
> How do i install DSSP for gromacs 5.1.1
> I am curently working on Centos
> Which version should i download and any commands to install dssp
>
> Thanks & Regards
> Sanket
> --
> 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.
>
-- 
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.

[gmx-users] DSSP Error

[masoud keramati]

Hi to all

first i run 'gmx do_dssp -s md.tpr -f md.xtc' i  go this error:
Fatal error:
DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP)

then i put dssp executable file in the path 'usr/local/bin/dssp'
and run following command : 'export DSSP=/usr/local/bin/dssp'
now when i run gmx do_dssp i get this error: 'Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.'
even with use of-ver option, i got the same error.
what can i do to solve this problem?

thanks for your help
-- 
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.

[gmx-users] DSSP Erorr

[masoud keramati]

Hi to all

first i run 'gmx do_dssp -s md.tpr -f md.xtc' i  go this error:
Fatal error:
DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP)

then i put dssp executable file in the path 'usr/local/bin/dssp'
and run following command : 'export DSSP=/usr/local/bin/dssp'
now when i run gmx do_dssp i get this error: 'Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.'
even with use of-ver option, i got the same error.
what can i do to solve this problem?

thanks for your help
-- 
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.

Re: [gmx-users] DSSP

[Justin Lemkul]

On 3/21/17 5:13 AM, Aishwarya Dhar wrote:

Following procedure I have used
1. Downloaded  http://swift.cmbi.ru.nl/gv/dssp/
dssp-2.0.4-linux-i386 and renamed it dssp

2.made dssp  executable  and moved it to usr/local/bin

3.Then ran the command from the current location where the tpr and trr
files are present do_dssp -s  md.tpr -f md.trr -o ss.xpm  -ver 2.0

4.There are 91 residues in your selected group dssp cmd='/usr/local/bin/dssp
-i ddixopnV -o dd4YitS9 > /dev/null 2> /dev/null'
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Back Off! I just backed up ddixopnV to ./#ddixopnV.1#

It seems that the run is going on for two weeks and dssp analysis couldnt
be done



How many frames did you save?  do_dssp is a very slow program (it's just a 
wrapper to call dssp) and if you have tons of frames, it will take a long time. 
You can always list the files in the directory in which do_dssp is operating and 
you should see temporary files prefixed with "dd" being created and over-written.


You can always test whether or not do_dssp is working by passing it a single 
frame to -f, rather than waiting for a very expensive .trr file to be processed 
in full.


-Justin

















Thanks




Sincerely

Aishwarya Dhar



--
==

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

==
--
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.

Re: [gmx-users] DSSP

[Aishwarya Dhar]

Dear Sir,

Now, I have used one single frame by using this command and tried do_dssp
trjconv -f md.xtc -o md_1_frame.xtc -b 0 -e 0
do_dssp -s  md.tpr -f md_1_frame.xtc -o ss.xpm   -sc scount.xvg

Now  I get the following  and this is still going on

here are 91 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i ddlpFBB7 -o ddZv4Q6o > /dev/null 2>
/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddlpFBB7 to ./#ddlpFBB7.1#


Thanks

Sincerely

Aishwarya Dhar

On Tue, Mar 21, 2017 at 5:51 PM, Justin Lemkul  wrote:

>
>
> On 3/21/17 5:13 AM, Aishwarya Dhar wrote:
>
>> Following procedure I have used
>> 1. Downloaded  http://swift.cmbi.ru.nl/gv/dssp/
>> dssp-2.0.4-linux-i386 and renamed it dssp
>>
>> 2.made dssp  executable  and moved it to usr/local/bin
>>
>> 3.Then ran the command from the current location where the tpr and trr
>> files are present do_dssp -s  md.tpr -f md.trr -o ss.xpm  -ver 2.0
>>
>> 4.There are 91 residues in your selected group dssp
>> cmd='/usr/local/bin/dssp
>> -i ddixopnV -o dd4YitS9 > /dev/null 2> /dev/null'
>> trn version: GMX_trn_file (single precision)
>> Reading frame   0 time0.000
>> Back Off! I just backed up ddixopnV to ./#ddixopnV.1#
>>
>> It seems that the run is going on for two weeks and dssp analysis couldnt
>> be done
>>
>>
> How many frames did you save?  do_dssp is a very slow program (it's just a
> wrapper to call dssp) and if you have tons of frames, it will take a long
> time. You can always list the files in the directory in which do_dssp is
> operating and you should see temporary files prefixed with "dd" being
> created and over-written.
>
> You can always test whether or not do_dssp is working by passing it a
> single frame to -f, rather than waiting for a very expensive .trr file to
> be processed in full.
>
> -Justin
>
>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Thanks
>>
>>
>>
>>
>> Sincerely
>>
>> Aishwarya Dhar
>>
>>
> --
> ==
>
> 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
>
> ==
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Justin Lemkul]

On 5/25/17 12:08 PM, Mariusz Wierzbowski wrote:

Hi,

I would like to analyze secondary structure elements for my protein. I want to
do it with do_dssp command in gromacs. I am using gromacs on a plgrid platform.
The problem is that an error occurs:

Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv 
DSSP).

On other forums I have read about setting the environment with setenv or export
DSSP
but I think that these solutions are for programs on local system.



do_dssp is just a wrapper that calls the dssp program.  do_dssp always needs to 
know where the dssp binary is and it does that by assuming it is in 
/usr/local/bin/dssp unless you specify otherwise with an environment variable. 
That's true no matter what kind of computer you're running on.


-Justin

--
==

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

==
--
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.

[gmx-users] DSSP executable

[Deep kumar]

Hello All,

Can someone please help me get the "dssp" executable? For secondary
structure analysis.

I did this:

rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/

This downloaded all dssp pdb files but no executable. I am doing this
because I got the error on gromacs run.

Fatal error:

DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)

I would really appreciate help to resolve this problem.

Thanks
-- 
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.

[gmx-users] dssp plot

[marzieh dehghan]

Hi
Dear all
I used dssp plot to show the  alteration of secondary structure for special
residue numbers such as 100-200, but after calculation them, y axis of dssp
plot is started from zero instead from 100. please let me know which part
of m2p file should be changed to solve this problem.

thanks a lot
I am looking forward to getting your answer


;File 'scale.m2p' was generated
;By user: user1 (1000)
;On host: DELL7910
;At date: Thu Oct  5 22:05:56 2017

;
black&white  = no
linewidth= 1
titlefont= Times-Roman
titlefontsize= 20
legend   = yes
legendfont   = Times-Roman
legendlabel  =
legend2label =
legendfontsize   = 14
xbox = 0.08
ybox = 5
matrixspacing= 20.0
xoffset  = 0.0
yoffset  = 0.0
boxlinewidth = 1
ticklinewidth= 1
zerolinewidth= 1
x-lineat0value   = none
x-major  = 10
x-minor  = 5
x-firstmajor = 0
x-majorat0   = no
x-majorticklen   = 8.0
x-minorticklen   = 4.0
x-label  =
x-fontsize   = 16
x-font   = Times-Roman
x-tickfontsize   = 10
x-tickfont   = Helvetica
y-lineat0value   = none
y-major  =
y-minor  = 100
y-firstmajor = 0
y-majorat0   = no
y-majorticklen   = 8.0
y-minorticklen   = 4.0
y-label  =
y-fontsize   = 16
y-font   = Times-Roman
y-tickfontsize   = 10
y-tickfont   = Helvetica




-- 




*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
-- 
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.

Re: [gmx-users] DSSP

[Vytautas Rakeviius]

ftp://ftp.cmbi.ru.nl/pub/software/dssp/
There you can find windows .exe version of it.
 

On Tuesday, December 5, 2017, 7:38:44 AM GMT+2, Vidya R 
 wrote:  
 
 Hi gromacs users,

I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)

I want to download and install dssp tool.

How to proceed?


Thanks,
Vidya.R
-- 
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.
  
-- 
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.

Re: [gmx-users] DSSP

[João Henriques]

Hi!

This is not so much for you as it is for the other users and developers. I
think I found a problem with the DSSP code when compiling using the latest
boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
"include" directory of this new boost, and the compilation fails. The error
is reproducible if you instead use homebrew to install DSSP.

I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
email is active anymore. Hopefully it is, otherwise please let me know.

Best regards,
J

On Tue, Dec 5, 2017 at 6:38 AM, Vidya R  wrote:

> Hi gromacs users,
>
> I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
>
> I want to download and install dssp tool.
>
> How to proceed?
>
>
> Thanks,
> Vidya.R
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Vidya R]

I got the error

dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> /dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#

---
Program gmx do_dssp, VERSION 5.1.4
Source code file:
/cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/

gmx_do_dssp.c, line: 663

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option  .

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


On Tue, Dec 5, 2017 at 6:36 PM, João Henriques  wrote:

> Hi!
>
> This is not so much for you as it is for the other users and developers. I
> think I found a problem with the DSSP code when compiling using the latest
> boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> "include" directory of this new boost, and the compilation fails. The error
> is reproducible if you instead use homebrew to install DSSP.
>
> I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
> email is active anymore. Hopefully it is, otherwise please let me know.
>
> Best regards,
> J
>
> On Tue, Dec 5, 2017 at 6:38 AM, Vidya R  wrote:
>
> > Hi gromacs users,
> >
> > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> >
> > I want to download and install dssp tool.
> >
> > How to proceed?
> >
> >
> > Thanks,
> > Vidya.R
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[João Henriques]

Did you specify the DSSP version as the error message suggests? DSSP
version 2 has different syntax from the previous one. On the gromacs 5.1.4
do_dssp assumes that you're using version 2, but maybe yours is version 1.

P.S.: I am assuming you have done everything else correctly, i.e., you have
a working DSSP executable and you have exported that executable path as
$DSSP.

J

On Tue, Dec 5, 2017 at 3:41 PM, Vidya R  wrote:

> I got the error
>
> dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2> /dev/null'
> Reading frame   0 time0.000
> Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#
>
> ---
> Program gmx do_dssp, VERSION 5.1.4
> Source code file:
> /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/
>
> gmx_do_dssp.c, line: 663
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option  .
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <
> joao.m.a.henriq...@gmail.com
> > wrote:
>
> > Hi!
> >
> > This is not so much for you as it is for the other users and developers.
> I
> > think I found a problem with the DSSP code when compiling using the
> latest
> > boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> > "include" directory of this new boost, and the compilation fails. The
> error
> > is reproducible if you instead use homebrew to install DSSP.
> >
> > I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
> > email is active anymore. Hopefully it is, otherwise please let me know.
> >
> > Best regards,
> > J
> >
> > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R  wrote:
> >
> > > Hi gromacs users,
> > >
> > > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> > >
> > > I want to download and install dssp tool.
> > >
> > > How to proceed?
> > >
> > >
> > > Thanks,
> > > Vidya.R
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Vidya R]

Hi,

I have installed dssp version


*3.0.0-win32*

*What should be the command now?*

On Tue, Dec 5, 2017 at 10:08 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Did you specify the DSSP version as the error message suggests? DSSP
> version 2 has different syntax from the previous one. On the gromacs 5.1.4
> do_dssp assumes that you're using version 2, but maybe yours is version 1.
>
> P.S.: I am assuming you have done everything else correctly, i.e., you have
> a working DSSP executable and you have exported that executable path as
> $DSSP.
>
> J
>
> On Tue, Dec 5, 2017 at 3:41 PM, Vidya R  wrote:
>
> > I got the error
> >
> > dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2>
> /dev/null'
> > Reading frame   0 time0.000
> > Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#
> >
> > ---
> > Program gmx do_dssp, VERSION 5.1.4
> > Source code file:
> > /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/
> >
> > gmx_do_dssp.c, line: 663
> >
> > Fatal error:
> > Failed to execute command: Try specifying your dssp version with the -ver
> > option  .
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> > On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <
> > joao.m.a.henriq...@gmail.com
> > > wrote:
> >
> > > Hi!
> > >
> > > This is not so much for you as it is for the other users and
> developers.
> > I
> > > think I found a problem with the DSSP code when compiling using the
> > latest
> > > boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> > > "include" directory of this new boost, and the compilation fails. The
> > error
> > > is reproducible if you instead use homebrew to install DSSP.
> > >
> > > I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this
> > > email is active anymore. Hopefully it is, otherwise please let me know.
> > >
> > > Best regards,
> > > J
> > >
> > > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R 
> wrote:
> > >
> > > > Hi gromacs users,
> > > >
> > > > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> > > >
> > > > I want to download and install dssp tool.
> > > >
> > > > How to proceed?
> > > >
> > > >
> > > > Thanks,
> > > > Vidya.R
> > > > --
> > > > 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.
> > > >
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP

[Mark Abraham]

Hi,

Please follow the instructions at gmx do_dssp -h

Mark

On Wed, Dec 6, 2017, 3:52 AM Vidya R  wrote:

> Hi,
>
> I have installed dssp version
>
>
> *3.0.0-win32*
>
> *What should be the command now?*
>
> On Tue, Dec 5, 2017 at 10:08 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > Did you specify the DSSP version as the error message suggests? DSSP
> > version 2 has different syntax from the previous one. On the gromacs
> 5.1.4
> > do_dssp assumes that you're using version 2, but maybe yours is version
> 1.
> >
> > P.S.: I am assuming you have done everything else correctly, i.e., you
> have
> > a working DSSP executable and you have exported that executable path as
> > $DSSP.
> >
> > J
> >
> > On Tue, Dec 5, 2017 at 3:41 PM, Vidya R  wrote:
> >
> > > I got the error
> > >
> > > dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2>
> > /dev/null'
> > > Reading frame   0 time0.000
> > > Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#
> > >
> > > ---
> > > Program gmx do_dssp, VERSION 5.1.4
> > > Source code file:
> > > /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/
> > >
> > > gmx_do_dssp.c, line: 663
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option  .
> > >
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > >
> > > On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <
> > > joao.m.a.henriq...@gmail.com
> > > > wrote:
> > >
> > > > Hi!
> > > >
> > > > This is not so much for you as it is for the other users and
> > developers.
> > > I
> > > > think I found a problem with the DSSP code when compiling using the
> > > latest
> > > > boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> > > > "include" directory of this new boost, and the compilation fails. The
> > > error
> > > > is reproducible if you instead use homebrew to install DSSP.
> > > >
> > > > I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure
> this
> > > > email is active anymore. Hopefully it is, otherwise please let me
> know.
> > > >
> > > > Best regards,
> > > > J
> > > >
> > > > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R 
> > wrote:
> > > >
> > > > > Hi gromacs users,
> > > > >
> > > > > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> > > > >
> > > > > I want to download and install dssp tool.
> > > > >
> > > > > How to proceed?
> > > > >
> > > > >
> > > > > Thanks,
> > > > > Vidya.R
> > > > > --
> > > > > 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.
> > > > >
> > > > --
> > > > 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.
> > > >
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
> --
> 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.
-- 
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_Li

Re: [gmx-users] DSSP

[João Henriques]

There's no DSSP version 3 that I know of. That can't be right.

J

On Tue, Dec 5, 2017 at 5:52 PM, Vidya R  wrote:

> Hi,
>
> I have installed dssp version
>
>
> *3.0.0-win32*
>
> *What should be the command now?*
>
> On Tue, Dec 5, 2017 at 10:08 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > Did you specify the DSSP version as the error message suggests? DSSP
> > version 2 has different syntax from the previous one. On the gromacs
> 5.1.4
> > do_dssp assumes that you're using version 2, but maybe yours is version
> 1.
> >
> > P.S.: I am assuming you have done everything else correctly, i.e., you
> have
> > a working DSSP executable and you have exported that executable path as
> > $DSSP.
> >
> > J
> >
> > On Tue, Dec 5, 2017 at 3:41 PM, Vidya R  wrote:
> >
> > > I got the error
> > >
> > > dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2>
> > /dev/null'
> > > Reading frame   0 time0.000
> > > Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#
> > >
> > > ---
> > > Program gmx do_dssp, VERSION 5.1.4
> > > Source code file:
> > > /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/
> > >
> > > gmx_do_dssp.c, line: 663
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option  .
> > >
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > >
> > > On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <
> > > joao.m.a.henriq...@gmail.com
> > > > wrote:
> > >
> > > > Hi!
> > > >
> > > > This is not so much for you as it is for the other users and
> > developers.
> > > I
> > > > think I found a problem with the DSSP code when compiling using the
> > > latest
> > > > boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> > > > "include" directory of this new boost, and the compilation fails. The
> > > error
> > > > is reproducible if you instead use homebrew to install DSSP.
> > > >
> > > > I've emailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure
> this
> > > > email is active anymore. Hopefully it is, otherwise please let me
> know.
> > > >
> > > > Best regards,
> > > > J
> > > >
> > > > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R 
> > wrote:
> > > >
> > > > > Hi gromacs users,
> > > > >
> > > > > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> > > > >
> > > > > I want to download and install dssp tool.
> > > > >
> > > > > How to proceed?
> > > > >
> > > > >
> > > > > Thanks,
> > > > > Vidya.R
> > > > > --
> > > > > 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.
> > > > >
> > > > --
> > > > 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.
> > > >
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
> --
> 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.
>
-- 
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/

[gmx-users] DSSP installation

[spss4]

  
Hii all
I want to calculate the number of helical contain of protein. For that I
tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
and exported the path to ./bashrc file
export DSSP=/usr/local/bin/dssp

Then when I was trying to use gmx do_dssp and select protein then the
following error comes

WARNING: You use DSSP version 3, which is not explicitly
supported by do_dssp. Assuming version 2 syntax.
 
dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
/dev/null'
trr version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#
 
---
Program:     gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
 
Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option

Then I tried using the version -ver 3 
But still the error comes.
Please help me to fix this problem.
Thanks

Sunipa Sarkar
 
--
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.

[gmx-users] DSSP regardin

[RAHUL SURESH]

Hi Users.

I have Performed dssp for 1000ns simulation. On converting the xpm to eps,
the axis are not visible to any extent. I have tried with different values
and I couldn't obtain a good image. Can anyone pass possible  suitable
commands for long simulations to obtain a satisfactory image?

-- 
*Regards,*
*Rahul *
-- 
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.

[gmx-users] dssp error

[Mario Andres Rodriguez Pineda]

Good afternoon.
I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4
for secondary structure analysis. When i try to run it i used this commad:

gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc
protssp.xvg

but gromacs send me this error:
Program: gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.

Can you help me to fix this error?
Thanks for your help


-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
1475*
-- 
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.

Re: [gmx-users] dssp

[Erik Marklund]

Hi,

dssp.exe? Are you sure that's the name of the file?

Kind regards,
Erik
 
Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 5 Jun 2014, at 10:40, Uma Devi  wrote:

> dear sir/madam
> i am new to gromacs. i am trying to install DSSP,i am having centos. i
> downloaded the DSSP and pasted it in /usr/local/bin directory
> while i am running it shows the following error
> 
> 
> Failed to execute command: /usr/local/bin/dssp.exe -na ddLV8RKo ddvXmynp >
> /dev/null 2> /dev/null
> 
> please help me to get the solutions.
> thanks in advance
> 
> uma
> -- 
> 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.

-- 
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.

Re: [gmx-users] dssp

[Uma Devi]

Thanks Mr. Erik for your kind reply.
yes the file name is dssp.exe only


On Thu, Jun 5, 2014 at 3:10 PM, Uma Devi  wrote:

> dear sir/madam
> i am new to gromacs. i am trying to install DSSP,i am having centos. i
> downloaded the DSSP and pasted it in /usr/local/bin directory
> while i am running it shows the following error
>
>
> Failed to execute command: /usr/local/bin/dssp.exe -na ddLV8RKo ddvXmynp >
> /dev/null 2> /dev/null
>
> please help me to get the solutions.
> thanks in advance
>
> uma
>
-- 
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.

Re: [gmx-users] dssp

[Tsjerk Wassenaar]

Hi Uma,

What happens if you run dssp by itself on the command line?

Cheers,

Tsjerk


On Fri, Jun 6, 2014 at 5:13 AM, Uma Devi  wrote:

> Thanks Mr. Erik for your kind reply.
> yes the file name is dssp.exe only
>
>
> On Thu, Jun 5, 2014 at 3:10 PM, Uma Devi  wrote:
>
> > dear sir/madam
> > i am new to gromacs. i am trying to install DSSP,i am having centos. i
> > downloaded the DSSP and pasted it in /usr/local/bin directory
> > while i am running it shows the following error
> >
> >
> > Failed to execute command: /usr/local/bin/dssp.exe -na ddLV8RKo ddvXmynp
> >
> > /dev/null 2> /dev/null
> >
> > please help me to get the solutions.
> > thanks in advance
> >
> > uma
> >
> --
> 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.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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.

Re: [gmx-users] dssp

[Gurunath Katagi]

HI
please check version of the dssp that ur trying to use on CentOS. It could
be the case that its a window exec file ur trying to run on linux..

thank you
Gurunath


On Fri, Jun 6, 2014 at 11:35 AM, Tsjerk Wassenaar  wrote:

> Hi Uma,
>
> What happens if you run dssp by itself on the command line?
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, Jun 6, 2014 at 5:13 AM, Uma Devi  wrote:
>
> > Thanks Mr. Erik for your kind reply.
> > yes the file name is dssp.exe only
> >
> >
> > On Thu, Jun 5, 2014 at 3:10 PM, Uma Devi  wrote:
> >
> > > dear sir/madam
> > > i am new to gromacs. i am trying to install DSSP,i am having centos. i
> > > downloaded the DSSP and pasted it in /usr/local/bin directory
> > > while i am running it shows the following error
> > >
> > >
> > > Failed to execute command: /usr/local/bin/dssp.exe -na ddLV8RKo
> ddvXmynp
> > >
> > > /dev/null 2> /dev/null
> > >
> > > please help me to get the solutions.
> > > thanks in advance
> > >
> > > uma
> > >
> > --
> > 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.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> 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.
>
-- 
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.

[gmx-users] DSSP -regarding

[Uma Devi]

hi Tsjerk,
 thanks for your reply.sorry for the late reply. if i type the dssp -h it
shows the following message

DSSP 2.0.4 options:
  -h [ --help ] Display help message
  -i [ --input ] argInput file
  -o [ --output ] arg   Output file, use 'stdout' to output to screen
  -v [ --verbose ]  Verbose output
  --version Print version
  -d [ --debug ] argDebug level (for even more verbose output)


Examples:

To calculate the secondary structure for the file 1crn.pdb and
write the result to a file called 1crn.dssp, you type:

  dssp.exe -i 1crn.pdb -o 1crn.dssp
-- 
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.

[gmx-users] dssp 3.1.4

[Iman Katouzian]

Good day,

I have recently downloaded the latest dssp version and with the mkdssp
executable file as I type chmod +x dssp and run this code :
gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg
-tu ns

the process starts but no output is created after even 1 day 
my Gormacs version is 2019.3 and even earlier versions of dssp does not
work and give me the same result. Till now I have tested this process on 3
computers having GROMACS 2019.3 on them.

Can someone help me with this issue?
Many thanks.

-- 

*Iman Katouzian*

*Ph.D.** candidate of Food Process Engineering*

*Faculty of Food Science and Technology*

*University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
-- 
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.

[gmx-users] DSSP secondary structure

[mohammad r]

Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein 
during the simulation but the resolution of the resulted .xpm file is very low. 
how can I increase its resolution?
Thank you, Mohammad.
-- 
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.

Re: [gmx-users] DSSP Error

[Nikhil Maroli]

Hi,
Please download the current version and try.You can find solution and more
details here in the mailing list.See the Archive.
-- 
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.

Re: [gmx-users] DSSP executable

[Mark Abraham]

Hi,

You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first two
sentences are useful for you ;-)

Mark

On Mon, Sep 11, 2017 at 5:05 PM Deep kumar 
wrote:

> Hello All,
>
> Can someone please help me get the "dssp" executable? For secondary
> structure analysis.
>
> I did this:
>
> rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/
>
> This downloaded all dssp pdb files but no executable. I am doing this
> because I got the error on gromacs run.
>
> Fatal error:
>
> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
>
> I would really appreciate help to resolve this problem.
>
> Thanks
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP executable

[Deep kumar]

Thanks Marc!

On Mon, Sep 11, 2017 at 6:07 PM, Mark Abraham 
wrote:

> Hi,
>
> You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first
> two
> sentences are useful for you ;-)
>
> Mark
>
> On Mon, Sep 11, 2017 at 5:05 PM Deep kumar 
> wrote:
>
> > Hello All,
> >
> > Can someone please help me get the "dssp" executable? For secondary
> > structure analysis.
> >
> > I did this:
> >
> > rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/
> >
> > This downloaded all dssp pdb files but no executable. I am doing this
> > because I got the error on gromacs run.
> >
> > Fatal error:
> >
> > DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
> >
> > I would really appreciate help to resolve this problem.
> >
> > Thanks
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP installation

[João Henriques]

The output is telling you what is wrong. Gromacs doesn't support version 3.
Install either version 1 or 2. In fact, I didn't even know there was a
version 3 of DSSP, where did you get it? It certainly isn't on the official
website (http://swift.cmbi.ru.nl/gv/dssp/).

J



On Fri, Dec 8, 2017 at 4:04 PM,  wrote:

>
> Hii all
> I want to calculate the number of helical contain of protein. For that I
> tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
> tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
> and exported the path to ./bashrc file
> export DSSP=/usr/local/bin/dssp
>
> Then when I was trying to use gmx do_dssp and select protein then the
> following error comes
>
> WARNING: You use DSSP version 3, which is not explicitly
> supported by do_dssp. Assuming version 2 syntax.
>
> dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
> /dev/null'
> trr version: GMX_trn_file (single precision)
> Reading frame   0 time0.000
> Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#
>
> ---
> Program: gmx do_dssp, version 2016.3
> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option
>
> Then I tried using the version -ver 3
> But still the error comes.
> Please help me to fix this problem.
> Thanks
>
> Sunipa Sarkar
>
> --
> 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.
-- 
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.

Re: [gmx-users] DSSP installation

[spss4]

 - Message from João Henriques 
-
    Date: Sat, 9 Dec 2017 11:29:41 +0100
    From: João Henriques 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DSSP installation
      To: gmx-us...@gromacs.org


The output is telling you what is wrong. Gromacs doesn't support version
3.
Install either version 1 or 2. In fact, I didn't even know there was a
version 3 of DSSP, where did you get it? It certainly isn't on the
official
website (http://swift.cmbi.ru.nl/gv/dssp/).

J

Hii
I tried with version 2 but same problem was there. I thought gromacs
2016.3 is the latest one thats why version 2 is not supported. So I
downloaded version
3 from this link   ftp://ftp.cmbi.ru.nl/pub/software/dssp/ . I am very
new in this field. Please correct me if I am doing something wrong.
thanks

sunipa sarkar

On Fri, Dec 8, 2017 at 4:04 PM,  wrote:


Hii all
I want to calculate the number of helical contain of protein. For that I
tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
and exported the path to ./bashrc file
export DSSP=/usr/local/bin/dssp

Then when I was trying to use gmx do_dssp and select protein then the
following error comes

WARNING: You use DSSP version 3, which is not explicitly
supported by do_dssp. Assuming version 2 syntax.

dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
/dev/null'
trr version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#

---
Program:     gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)

Fatal error:
Failed to execute command: Try specifying your dssp version with the

-ver

option

Then I tried using the version -ver 3
But still the error comes.
Please help me to fix this problem.
Thanks

Sunipa Sarkar

--
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.


--
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
visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or send a mail to gmx-users-requ...@gromacs.org.


- End message from João Henriques  -
--
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.

Re: [gmx-users] DSSP installation

[spss4]

 - Message from João Henriques 
-
    Date: Sat, 9 Dec 2017 11:29:41 +0100
    From: João Henriques 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DSSP installation
      To: gmx-us...@gromacs.org


The output is telling you what is wrong. Gromacs doesn't support version
3.
Install either version 1 or 2. In fact, I didn't even know there was a
version 3 of DSSP, where did you get it? It certainly isn't on the
official
website (http://swift.cmbi.ru.nl/gv/dssp/).

J

When I try version 2 there is no warning but only this fatal error comes



Program:     gmx do_dssp, version 2016.3
 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
  
 Fatal error:
 Failed to execute command: Try specifying your dssp version with the -ver
 option.

I have have exported the path in bashrc file though this error comes.
Please give any suggestion.

Sunipa


 

On Fri, Dec 8, 2017 at 4:04 PM,  wrote:


Hii all
I want to calculate the number of helical contain of protein. For that I
tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
and exported the path to ./bashrc file
export DSSP=/usr/local/bin/dssp

Then when I was trying to use gmx do_dssp and select protein then the
following error comes

WARNING: You use DSSP version 3, which is not explicitly
supported by do_dssp. Assuming version 2 syntax.

dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
/dev/null'
trr version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#

---
Program:     gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)

Fatal error:
Failed to execute command: Try specifying your dssp version with the

-ver

option

Then I tried using the version -ver 3
But still the error comes.
Please help me to fix this problem.
Thanks

Sunipa Sarkar

--
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.


--
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
visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or send a mail to gmx-users-requ...@gromacs.org.


- End message from João Henriques  -
--
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.

Re: [gmx-users] DSSP installation

[João Henriques]

I already told you, use a DSSP executable that is compatible (versions 1 or
2) and pass the right version number to the -ver flag of do_dssp.

J

On Sat, Dec 9, 2017 at 1:06 PM,  wrote:

>  - Message from João Henriques 
> -
> Date: Sat, 9 Dec 2017 11:29:41 +0100
> From: João Henriques 
> Reply-To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] DSSP installation
>   To: gmx-us...@gromacs.org
>
> The output is telling you what is wrong. Gromacs doesn't support version
>> 3.
>> Install either version 1 or 2. In fact, I didn't even know there was a
>> version 3 of DSSP, where did you get it? It certainly isn't on the
>> official
>> website (http://swift.cmbi.ru.nl/gv/dssp/).
>>
>> J
>>
>> When I try version 2 there is no warning but only this fatal error comes
>>
>
>
> Program: gmx do_dssp, version 2016.3
>  Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>
>  Fatal error:
>  Failed to execute command: Try specifying your dssp version with the -ver
>  option.
>
> I have have exported the path in bashrc file though this error comes.
> Please give any suggestion.
>
> Sunipa
>
>
>
>>
>> On Fri, Dec 8, 2017 at 4:04 PM,  wrote:
>>
>> Hii all
>>> I want to calculate the number of helical contain of protein. For that I
>>> tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
>>> tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
>>> and exported the path to ./bashrc file
>>> export DSSP=/usr/local/bin/dssp
>>>
>>> Then when I was trying to use gmx do_dssp and select protein then the
>>> following error comes
>>>
>>> WARNING: You use DSSP version 3, which is not explicitly
>>> supported by do_dssp. Assuming version 2 syntax.
>>>
>>> dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
>>> /dev/null'
>>> trr version: GMX_trn_file (single precision)
>>> Reading frame   0 time0.000
>>> Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#
>>>
>>> ---
>>> Program: gmx do_dssp, version 2016.3
>>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>>>
>>> Fatal error:
>>> Failed to execute command: Try specifying your dssp version with the
>>>
>> -ver
>
>> option
>>>
>>> Then I tried using the version -ver 3
>>> But still the error comes.
>>> Please help me to fix this problem.
>>> Thanks
>>>
>>> Sunipa Sarkar
>>>
>>> --
>>> 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.
>>>
>>
>> --
>> 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
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-requ...@gromacs.org.
>>
>
> - End message from João Henriques  -
> --
> 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.
>
-- 
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.

[gmx-users] dssp excutable-error

[marzieh dehghan]

Dear all
I installed dssp software on ubuntu version 12.04 in the /usr/local/bin,
when I run the following command "*sudo find / -name dssp*" it showed the
mentioned pathway, but when I apply the following comand "*gmx do_dssp -f
xtc -s tpr -o xpm -sc xvg -tu ns*"

I confronted to this error:
*"failed to execute command: try specifying your dssp version with the -ver
option" *

please let me know how to solve this problem.

Thanks in advances.
Best wishes.
Marzieh
-- 




*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
-- 
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.

Re: [gmx-users] DSSP regardin

[Mateusz Bieniek]

Hi Rahul,

I've run into a similar issue a year ago. It is possible to configure gmx
with the extra configuration file (as described in the documentation) to
get this right.

However, I found it to be archaic and wrote my own quick DSSP visualiser in
matplotlib.

I am planning to improve the code and release it with the next paper, but
for now I attach the simple one.

Note that not all dssp letters/secondary structures have been added, so you
might need to add more colors:
colors = {
coil_char: "#FF",
bsheet_char: "#FF",
bbridge_char: "#00",
bend_char: "#008000",
turn_char: "#00",
three_helix_char: "#808080",
  }


Hope this helps, Mat




On Fri, 15 Mar 2019 at 17:06, RAHUL SURESH  wrote:

> Hi Users.
>
> I have Performed dssp for 1000ns simulation. On converting the xpm to eps,
> the axis are not visible to any extent. I have tried with different values
> and I couldn't obtain a good image. Can anyone pass possible  suitable
> commands for long simulations to obtain a satisfactory image?
>
> --
> *Regards,*
> *Rahul *
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP regardin

[RAHUL SURESH]

Thank you so much Mr Mat.

That was very usual.

On Sat, Mar 16, 2019 at 10:27 PM Mateusz Bieniek 
wrote:

> Hi Rahul,
>
> I've run into a similar issue a year ago. It is possible to configure gmx
> with the extra configuration file (as described in the documentation) to
> get this right.
>
> However, I found it to be archaic and wrote my own quick DSSP visualiser in
> matplotlib.
>
> I am planning to improve the code and release it with the next paper, but
> for now I attach the simple one.
>
> Note that not all dssp letters/secondary structures have been added, so you
> might need to add more colors:
> colors = {
> coil_char: "#FF",
> bsheet_char: "#FF",
> bbridge_char: "#00",
> bend_char: "#008000",
> turn_char: "#00",
> three_helix_char: "#808080",
>   }
>
>
> Hope this helps, Mat
>
>
>
>
> On Fri, 15 Mar 2019 at 17:06, RAHUL SURESH 
> wrote:
>
> > Hi Users.
> >
> > I have Performed dssp for 1000ns simulation. On converting the xpm to
> eps,
> > the axis are not visible to any extent. I have tried with different
> values
> > and I couldn't obtain a good image. Can anyone pass possible  suitable
> > commands for long simulations to obtain a satisfactory image?
> >
> > --
> > *Regards,*
> > *Rahul *
> > --
> > 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.
> >
> --
> 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.



-- 
*Regards,*
*Rahul *
-- 
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.

Re: [gmx-users] dssp error

[Qinghua Liao]

Hello,

Just follow the suggestion by adding "-ver 2" to your command.


All the best,
Qinghua

On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote:

Good afternoon.
I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4
for secondary structure analysis. When i try to run it i used this commad:

gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc
protssp.xvg

but gromacs send me this error:
Program: gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.

Can you help me to fix this error?
Thanks for your help




--
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.

Re: [gmx-users] dssp error

[Mario Andres Rodriguez Pineda]

gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns
-sc cbd211ssp.xvg -ver 2

Program: gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.


Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao 
escreveu:

> Hello,
>
> Just follow the suggestion by adding "-ver 2" to your command.
>
>
> All the best,
> Qinghua
>
> On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote:
> > Good afternoon.
> > I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4
> > for secondary structure analysis. When i try to run it i used this
> commad:
> >
> > gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc
> > protssp.xvg
> >
> > but gromacs send me this error:
> > Program: gmx do_dssp, version 2016.3
> > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
> >
> > Fatal error:
> > Failed to execute command: Try specifying your dssp version with the -ver
> > option.
> >
> > Can you help me to fix this error?
> > Thanks for your help
> >
> >
>
> --
> 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.
>


-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
1475*
-- 
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.

Re: [gmx-users] dssp error

[Qinghua Liao]

Have a check the installation of DSSP,
did you set the variable DSSP for do_dssp?


All the best,
Qinghua


On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote:

gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns
-sc cbd211ssp.xvg -ver 2

Program: gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.


Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao 
escreveu:


Hello,

Just follow the suggestion by adding "-ver 2" to your command.


All the best,
Qinghua

On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote:

Good afternoon.
I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4
for secondary structure analysis. When i try to run it i used this

commad:

gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc
protssp.xvg

but gromacs send me this error:
Program: gmx do_dssp, version 2016.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.

Can you help me to fix this error?
Thanks for your help



--
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.





--
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.

Re: [gmx-users] dssp error

[Mario Andres Rodriguez Pineda]

I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an
executable

Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao 
escreveu:

> Have a check the installation of DSSP,
> did you set the variable DSSP for do_dssp?
>
>
> All the best,
> Qinghua
>
>
> On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote:
> > gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu
> ns
> > -sc cbd211ssp.xvg -ver 2
> >
> > Program: gmx do_dssp, version 2016.3
> > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
> >
> > Fatal error:
> > Failed to execute command: Try specifying your dssp version with the -ver
> > option.
> >
> >
> > Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao  >
> > escreveu:
> >
> >> Hello,
> >>
> >> Just follow the suggestion by adding "-ver 2" to your command.
> >>
> >>
> >> All the best,
> >> Qinghua
> >>
> >> On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote:
> >>> Good afternoon.
> >>> I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP
> 2.0.4
> >>> for secondary structure analysis. When i try to run it i used this
> >> commad:
> >>> gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns
> -sc
> >>> protssp.xvg
> >>>
> >>> but gromacs send me this error:
> >>> Program: gmx do_dssp, version 2016.3
> >>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
> >>>
> >>> Fatal error:
> >>> Failed to execute command: Try specifying your dssp version with the
> -ver
> >>> option.
> >>>
> >>> Can you help me to fix this error?
> >>> Thanks for your help
> >>>
> >>>
> >> --
> >> 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.
> >>
> >
>
> --
> 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.



-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
1475*
-- 
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.

Re: [gmx-users] dssp error

[Soham Sarkar]

sometimes it happened if there is any residue that is unknown to DSSP, then
it might show this kind of error. I faced it once.

On Fri, Mar 22, 2019 at 1:10 AM Mario Andres Rodriguez Pineda <
mand...@iq.usp.br> wrote:

> I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an
> executable
>
> Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao 
> escreveu:
>
> > Have a check the installation of DSSP,
> > did you set the variable DSSP for do_dssp?
> >
> >
> > All the best,
> > Qinghua
> >
> >
> > On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote:
> > > gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm
> -tu
> > ns
> > > -sc cbd211ssp.xvg -ver 2
> > >
> > > Program: gmx do_dssp, version 2016.3
> > > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option.
> > >
> > >
> > > Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao <
> scorpio.l...@gmail.com
> > >
> > > escreveu:
> > >
> > >> Hello,
> > >>
> > >> Just follow the suggestion by adding "-ver 2" to your command.
> > >>
> > >>
> > >> All the best,
> > >> Qinghua
> > >>
> > >> On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote:
> > >>> Good afternoon.
> > >>> I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP
> > 2.0.4
> > >>> for secondary structure analysis. When i try to run it i used this
> > >> commad:
> > >>> gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns
> > -sc
> > >>> protssp.xvg
> > >>>
> > >>> but gromacs send me this error:
> > >>> Program: gmx do_dssp, version 2016.3
> > >>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
> > >>>
> > >>> Fatal error:
> > >>> Failed to execute command: Try specifying your dssp version with the
> > -ver
> > >>> option.
> > >>>
> > >>> Can you help me to fix this error?
> > >>> Thanks for your help
> > >>>
> > >>>
> > >> --
> > >> 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.
> > >>
> > >
> >
> > --
> > 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.
>
>
>
> --
> *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
> *Estudiante Doctorado en Biotecnología*
>
> *UNAL- MEDELLÍN/ IQ- USP*
>
> *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
> *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091
> 1475*
> --
> 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.
-- 
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.

[gmx-users] dssp installation error

[elham tazikeh]

dear gromacs users
when i run do_dssp program 4.5 and 4.6
i saw below error
plz help me

progran do_dssp, version 4.5.3
source code file:do_dsso.c, line: 521

fatal error:
failed to execute command: /usr/local/bin/dssp -na dd5iLsk0 ddj8721A >
/dev/null2> /dev/null

best regards
elham tazikeh
-- 
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.

Re: [gmx-users] dssp 3.1.4

[Mark Abraham]

Hi,

Do check out gmx do_dssp -h and make sure your dssp binary is the right
version, with executable permissions, in the right place (or alternatively
the appropriate environment variable is set, so that do_dssp can find dssp)

Mark

On Fri, 1 May 2020 at 18:47, Iman Katouzian  wrote:

> Good day,
>
> I have recently downloaded the latest dssp version and with the mkdssp
> executable file as I type chmod +x dssp and run this code :
> gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg
> -tu ns
>
> the process starts but no output is created after even 1 day 
> my Gormacs version is 2019.3 and even earlier versions of dssp does not
> work and give me the same result. Till now I have tested this process on 3
> computers having GROMACS 2019.3 on them.
>
> Can someone help me with this issue?
> Many thanks.
>
> --
>
> *Iman Katouzian*
>
> *Ph.D.** candidate of Food Process Engineering*
>
> *Faculty of Food Science and Technology*
>
> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/13/16 1:33 AM, mohammad r wrote:

Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein 
during the simulation but the resolution of the resulted .xpm file is very low. how can I 
increase its resolution?


You can adjust the matrix proportions with an .m2p file passed to xpm2ps -di. 
These are almost always necessary as there are many more frames than residues in 
the protein, usually an order of magnitude or more.


-Justin

--
==

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

==
--
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.

Re: [gmx-users] DSSP secondary structure

[mohammad r]

Thank you Justin,
I used xpm2ps command with below m2p file but the resolution was not changed. 
I've attached the xpm file, even the legend can't be seen.is there anyway to 
get the result file in pdf format?
m2p file (I found it in the gromacs website):
black&white = no ; Obsoletetitlefont = Times‐Roman ; A PostScript 
Fonttitlefontsize = 20 ; Font size (pt)legend = yes ; Show the legendlegendfont 
= Times‐Roman ; A PostScript Fontlegendlabel = ; Used when there is none in the 
.xpmlegend2label = ; Used when merging two xpm'slegendfontsize = 14 ; Font size 
(pt)xbox = 2.0 ; x‐size of a matrix elementybox = 2.0 ; y‐size of a matrix 
elementmatrixspacing = 20.0 ; Space between 2 matricesxoffset = 0.0 ; Between 
matrix and bounding boxyoffset = 0.0 ; Between matrix and bounding boxx‐major = 
20 ; Major ticks on x axis every .. framesx‐minor = 5 ; Id. Minor 
ticksx‐firstmajor = 0 ; First frame for major tickx‐majorat0 = no ; Major tick 
at first framex‐majorticklen = 8.0 ; x‐majorticklengthx‐minorticklen = 4.0 ; 
x‐minorticklengthx‐label = ; Used when there is none in the .xpmx‐fontsize = 16 
; Font size (pt)x‐font = Times‐Roman ; A PostScript Fontx‐tickfontsize = 10 ; 
Font size (pt)x‐tickfont = Helvetica ; A PostScript Fonty‐major = 20y‐minor = 
5y‐firstmajor = 0y‐majorat0 = noy‐majorticklen = 8.0y‐minorticklen = 4.0y‐label 
=y‐fontsize = 16y‐font = Times‐Romany‐tickfontsize = 10y‐tickfont = Helvetica
 

On Saturday, February 13, 2016 9:44 PM, Justin Lemkul  
wrote:
 

 

On 2/13/16 1:33 AM, mohammad r wrote:
> Hi,
> I used the "gmx do_dssp" command to get the secondary structure of the 
> protein during the simulation but the resolution of the resulted .xpm file is 
> very low. how can I increase its resolution?

You can adjust the matrix proportions with an .m2p file passed to xpm2ps -di. 
These are almost always necessary as there are many more frames than residues 
in 
the protein, usually an order of magnitude or more.

-Justin

-- 
==

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

==


  -- 
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.

Re: [gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/14/16 1:54 AM, mohammad r wrote:

Thank you Justin,

I used xpm2ps command with below m2p file but the resolution was not changed.
I've attached the xpm file, even the legend can't be seen.
is there anyway to get the result file in pdf format?

m2p file (I found it in the gromacs website):




xbox = 2.0 ; x‐size of a matrix element
ybox = 2.0 ; y‐size of a matrix element


You have a rectangular matrix, with the x-dimension being much longer than the 
y-dimension.  If you set these two values to be the same, what happens to the 
size of the rectangle?  It gets uniformly scaled.  So naturally that 
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.


-Justin

--
==

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

==
--
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.

Re: [gmx-users] DSSP secondary structure

[mohammad r]

I changed and reduced the ratio but the xpm file was not changed at all.
 

On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  wrote:
 

 

On 2/14/16 1:54 AM, mohammad r wrote:
> Thank you Justin,
>
> I used xpm2ps command with below m2p file but the resolution was not changed.
> I've attached the xpm file, even the legend can't be seen.
> is there anyway to get the result file in pdf format?
>
> m2p file (I found it in the gromacs website):
>

> xbox = 2.0 ; x‐size of a matrix element
> ybox = 2.0 ; y‐size of a matrix element

You have a rectangular matrix, with the x-dimension being much longer than the 
y-dimension.  If you set these two values to be the same, what happens to the 
size of the rectangle?  It gets uniformly scaled.  So naturally that 
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.

-Justin

-- 
==

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

==
-- 
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.

  
-- 
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.

Re: [gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/15/16 1:31 AM, mohammad r wrote:

I changed and reduced the ratio but the xpm file was not changed at all.



Unfortunately there's not much I can tell you here because this is rather 
cryptic.  It's illogical to get the same output with different input.  You can 
calculate exactly what values to use based on the number of residues in the 
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to 
fit some nicely shaped rectangle of defined proportions.


-Justin



 On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  
wrote:




On 2/14/16 1:54 AM, mohammad r wrote:

Thank you Justin,

I used xpm2ps command with below m2p file but the resolution was not changed.
I've attached the xpm file, even the legend can't be seen.
is there anyway to get the result file in pdf format?

m2p file (I found it in the gromacs website):




xbox = 2.0 ; x‐size of a matrix element
ybox = 2.0 ; y‐size of a matrix element


You have a rectangular matrix, with the x-dimension being much longer than the
y-dimension.  If you set these two values to be the same, what happens to the
size of the rectangle?  It gets uniformly scaled.  So naturally that
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.

-Justin



--
==

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

==
--
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.

Re: [gmx-users] DSSP secondary structure

[mohammad r]

Thank you Justin,
 I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any 
way to calculate the percentage of a-helical structure of a protein during 
simulation? Indeed DSSP visualize it but I want to calculate it exactly.
Thanks, Mohammad.
 

On Monday, February 15, 2016 6:31 PM, Justin Lemkul  wrote:
 

 

On 2/15/16 1:31 AM, mohammad r wrote:
> I changed and reduced the ratio but the xpm file was not changed at all.
>

Unfortunately there's not much I can tell you here because this is rather 
cryptic.  It's illogical to get the same output with different input.  You can 
calculate exactly what values to use based on the number of residues in the 
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to 
fit some nicely shaped rectangle of defined proportions.

-Justin

>
>      On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  
>wrote:
>
>
>
>
> On 2/14/16 1:54 AM, mohammad r wrote:
>> Thank you Justin,
>>
>> I used xpm2ps command with below m2p file but the resolution was not changed.
>> I've attached the xpm file, even the legend can't be seen.
>> is there anyway to get the result file in pdf format?
>>
>> m2p file (I found it in the gromacs website):
>>
>
>> xbox = 2.0 ; x‐size of a matrix element
>> ybox = 2.0 ; y‐size of a matrix element
>
> You have a rectangular matrix, with the x-dimension being much longer than the
> y-dimension.  If you set these two values to be the same, what happens to the
> size of the rectangle?  It gets uniformly scaled.  So naturally that
> accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.
>
> -Justin
>

-- 
==

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

==
-- 
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.

  
-- 
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.

Re: [gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/15/16 3:26 PM, mohammad r wrote:

Thank you Justin,
  I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any 
way to calculate the percentage of a-helical structure of a protein during 
simulation? Indeed DSSP visualize it but I want to calculate it exactly.


It should be at the end of the scount.xvg file.

-Justin


Thanks, Mohammad.


 On Monday, February 15, 2016 6:31 PM, Justin Lemkul  
wrote:




On 2/15/16 1:31 AM, mohammad r wrote:

I changed and reduced the ratio but the xpm file was not changed at all.



Unfortunately there's not much I can tell you here because this is rather
cryptic.  It's illogical to get the same output with different input.  You can
calculate exactly what values to use based on the number of residues in the
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to
fit some nicely shaped rectangle of defined proportions.

-Justin



   On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  
wrote:




On 2/14/16 1:54 AM, mohammad r wrote:

Thank you Justin,

I used xpm2ps command with below m2p file but the resolution was not changed.
I've attached the xpm file, even the legend can't be seen.
is there anyway to get the result file in pdf format?

m2p file (I found it in the gromacs website):




xbox = 2.0 ; x‐size of a matrix element
ybox = 2.0 ; y‐size of a matrix element


You have a rectangular matrix, with the x-dimension being much longer than the
y-dimension.  If you set these two values to be the same, what happens to the
size of the rectangle?  It gets uniformly scaled.  So naturally that
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.

-Justin





--
==

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

==
--
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.

[gmx-users] DSSP with custom residues

[Stephanie Jephthah]

Hi!

I'm simulating a protein conjugate and thus uses custom residues. Is there
any way to make the dssp program aware of the custom residues (and does it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.

Kind regards,
Stephanie Jephthah
-- 
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.

[gmx-users] DSSP with gmx 5.0.4

[RJ]

Dear gmx users,


I tried DSSP of both binary and .exe by renaming it as dssp 
(dssp-2.0.4-linux-amd64 & dssp-2.0.4-win32.exe from 
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in 
usr/local/bin/dssp.


set the excusable too (  "which dssp" /usr/local/bin/dssp).


Both of them gives  same error as follows; 
I also given a permission for dssp file "chmod 777 dssp" but still the error 
doesnt go. I use all new version but cant fix it? Any help plz.


gmx do_dssp -f prd_noPBC.xtc -s prd.tpr -sc scount.xvg -o ss.xpm -dt 10 -ver 2


Selected 5: 'MainChain'
There are 1446 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i ddiyE5RC -o ddPnxMzu > /dev/null 2> /dev/null'
Reading frame   0 time0.000   
Back Off! I just backed up ddiyE5RC to ./#ddiyE5RC.1#


---
Program gmx, VERSION 5.0.4
Source code file: /home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, 
line: 670


Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver 
option.
---
Program gmx, VERSION 5.0.4
Source code file: /home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, 
line: 670


Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver 
option.


 
-- 
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.

[gmx-users] dssp installation using cygwin

[Neha Gupta]

Hi gromacs users,

 I am using gromacs in windows  through cygwin

How to install dssp through cygwin?

Can anyone help?

Thanks,
Neha
-- 
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.

Re: [gmx-users] dssp excutable-error

[Mark Abraham]

Hi,

Have you followed the advice in gmx help do_dssp about setting the
environment variables? Did you install the correct version of dssp?

Mark

On Mon, Nov 12, 2018 at 11:43 PM marzieh dehghan 
wrote:

> Dear all
> I installed dssp software on ubuntu version 12.04 in the /usr/local/bin,
> when I run the following command "*sudo find / -name dssp*" it showed the
> mentioned pathway, but when I apply the following comand "*gmx do_dssp -f
> xtc -s tpr -o xpm -sc xvg -tu ns*"
>
> I confronted to this error:
> *"failed to execute command: try specifying your dssp version with the -ver
> option" *
>
> please let me know how to solve this problem.
>
> Thanks in advances.
> Best wishes.
> Marzieh
> --
>
>
>
>
> *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
> (IBB)University of Tehran, Tehran- Iran.*
> --
> 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.
>
-- 
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.

[gmx-users] DSSP graph re-scale

[SGR160055 Student]

Dear experts,

I have an issue to re-scale the x-axis on DSSP graph eps format for my 100
ns simulation time.

The x-axis of the graph became too compact until it can't be read clearly.

How should I solve this? Is there anyway to re-scale the graph for eps
format.

Your help is much appreciated. Thank you.



Regards,
Syah
-- 
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.

Re: [gmx-users] dssp installation error

[Erik Marklund]

Hi,

A: Did you set the DSSP environment variable to the dssp executable?
B: Does your dssp version match that which is expected by do_dssp?

Yours,
Erik

On 10 May 2014, at 19:39, elham tazikeh  wrote:

> dear gromacs users
> when i run do_dssp program 4.5 and 4.6
> i saw below error
> plz help me
> 
> progran do_dssp, version 4.5.3
> source code file:do_dsso.c, line: 521
> 
> fatal error:
> failed to execute command: /usr/local/bin/dssp -na dd5iLsk0 ddj8721A >
> /dev/null2> /dev/null
> 
> best regards
> elham tazikeh
> -- 
> 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.

-- 
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.

Re: [gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 8:57 AM, Stephanie Jephthah wrote:

Hi!

I'm simulating a protein conjugate and thus uses custom residues. Is there
any way to make the dssp program aware of the custom residues (and does it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.



If you've got custom residues as integral parts of the protein, they need to be 
defined as such in residuetypes.dat, or otherwise defined in a suitable custom 
index group.  Presumably you have to have done one or the other before running 
the simulation.  If the custom residues have normal amino acid backbone 
features, doing DSSP analysis makes sense.  If something is failing, run dssp 
directly, not via do_dssp, to determine if the failure is within dssp or do_dssp.


-Justin

--
==

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

==
--
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.

Re: [gmx-users] DSSP with custom residues

[leila salimi]

Hi Justin,

I am also busy by DSSP analysis. I am interested to know what the
difference between do_dssp and dssp is?

Regards,
Leila

On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:

>
>
> On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
>
>> Hi!
>>
>> I'm simulating a protein conjugate and thus uses custom residues. Is there
>> any way to make the dssp program aware of the custom residues (and does it
>> make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
>> assuming that the problem is not with do_dssp but with dssp, but please
>> correct me if I'm wrong.
>>
>>
> If you've got custom residues as integral parts of the protein, they need
> to be defined as such in residuetypes.dat, or otherwise defined in a
> suitable custom index group.  Presumably you have to have done one or the
> other before running the simulation.  If the custom residues have normal
> amino acid backbone features, doing DSSP analysis makes sense.  If
> something is failing, run dssp directly, not via do_dssp, to determine if
> the failure is within dssp or do_dssp.
>
> -Justin
>
> --
> ==
>
> 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
>
> ==
>
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 9:10 AM, leila salimi wrote:

Hi Justin,

I am also busy by DSSP analysis. I am interested to know what the
difference between do_dssp and dssp is?



dssp is a binary that actually carries out the DSSP analysis; it is not a 
GROMACS program but is downloaded from an external source.  do_dssp is a GROMACS 
module that is just a wrapper - it runs through a trajectory, pulls out the 
coordinates to a temporary file (those dd files that show up), passes those 
coordinates to dssp, and records the output.  GROMACS doesn't do secondary 
structure calculations natively, instead relying on dssp.


-Justin


Regards,
Leila

On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:




On 4/26/16 8:57 AM, Stephanie Jephthah wrote:


Hi!

I'm simulating a protein conjugate and thus uses custom residues. Is there
any way to make the dssp program aware of the custom residues (and does it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.



If you've got custom residues as integral parts of the protein, they need
to be defined as such in residuetypes.dat, or otherwise defined in a
suitable custom index group.  Presumably you have to have done one or the
other before running the simulation.  If the custom residues have normal
amino acid backbone features, doing DSSP analysis makes sense.  If
something is failing, run dssp directly, not via do_dssp, to determine if
the failure is within dssp or do_dssp.

-Justin

--
==

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

==

--
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

==
--
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.

Re: [gmx-users] DSSP with custom residues

[Stephanie Jephthah]

Ok. Thank you very much!

//Stephanie
Den 26 apr 2016 15:00 skrev "Justin Lemkul" :

>
>
> On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
>
>> Hi!
>>
>> I'm simulating a protein conjugate and thus uses custom residues. Is there
>> any way to make the dssp program aware of the custom residues (and does it
>> make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
>> assuming that the problem is not with do_dssp but with dssp, but please
>> correct me if I'm wrong.
>>
>>
> If you've got custom residues as integral parts of the protein, they need
> to be defined as such in residuetypes.dat, or otherwise defined in a
> suitable custom index group.  Presumably you have to have done one or the
> other before running the simulation.  If the custom residues have normal
> amino acid backbone features, doing DSSP analysis makes sense.  If
> something is failing, run dssp directly, not via do_dssp, to determine if
> the failure is within dssp or do_dssp.
>
> -Justin
>
> --
> ==
>
> 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
>
> ==
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP with custom residues

[leila salimi]

Thanks very much.

I have one problem, I am trying to use xpm2ps to plot the secondary
structure!
I used the m2p file from this link:

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)

My problem is that the plot is not correct. I tried different xbox and ybox
but it is not working and I got confused!

I have 10 residues and 400 ns time simulations ( 80001 frames).
For this file how can I  fix the xbox and ybox parameters?


Thanks in advance,

On Tue, Apr 26, 2016 at 3:12 PM, Justin Lemkul  wrote:

>
>
> On 4/26/16 9:10 AM, leila salimi wrote:
>
>> Hi Justin,
>>
>> I am also busy by DSSP analysis. I am interested to know what the
>> difference between do_dssp and dssp is?
>>
>>
> dssp is a binary that actually carries out the DSSP analysis; it is not a
> GROMACS program but is downloaded from an external source.  do_dssp is a
> GROMACS module that is just a wrapper - it runs through a trajectory, pulls
> out the coordinates to a temporary file (those dd files that show up),
> passes those coordinates to dssp, and records the output.  GROMACS doesn't
> do secondary structure calculations natively, instead relying on dssp.
>
> -Justin
>
>
> Regards,
>> Leila
>>
>> On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
>>>
>>> Hi!

 I'm simulating a protein conjugate and thus uses custom residues. Is
 there
 any way to make the dssp program aware of the custom residues (and does
 it
 make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
 assuming that the problem is not with do_dssp but with dssp, but please
 correct me if I'm wrong.


 If you've got custom residues as integral parts of the protein, they
>>> need
>>> to be defined as such in residuetypes.dat, or otherwise defined in a
>>> suitable custom index group.  Presumably you have to have done one or the
>>> other before running the simulation.  If the custom residues have normal
>>> amino acid backbone features, doing DSSP analysis makes sense.  If
>>> something is failing, run dssp directly, not via do_dssp, to determine if
>>> the failure is within dssp or do_dssp.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> 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
>>>
>>> ==
>>>
>>> --
>>> 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
>
> ==
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 1:10 PM, leila salimi wrote:

Thanks very much.

I have one problem, I am trying to use xpm2ps to plot the secondary
structure!
I used the m2p file from this link:

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)

My problem is that the plot is not correct. I tried different xbox and ybox
but it is not working and I got confused!

I have 10 residues and 400 ns time simulations ( 80001 frames).
For this file how can I  fix the xbox and ybox parameters?



Well, your x-axis will be 800x longer than your y-axis by default, so do the 
math (simple proportions!) to generate a suitably sized rectangular plot.


-Justin



Thanks in advance,

On Tue, Apr 26, 2016 at 3:12 PM, Justin Lemkul  wrote:




On 4/26/16 9:10 AM, leila salimi wrote:


Hi Justin,

I am also busy by DSSP analysis. I am interested to know what the
difference between do_dssp and dssp is?



dssp is a binary that actually carries out the DSSP analysis; it is not a
GROMACS program but is downloaded from an external source.  do_dssp is a
GROMACS module that is just a wrapper - it runs through a trajectory, pulls
out the coordinates to a temporary file (those dd files that show up),
passes those coordinates to dssp, and records the output.  GROMACS doesn't
do secondary structure calculations natively, instead relying on dssp.

-Justin


Regards,

Leila

On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:




On 4/26/16 8:57 AM, Stephanie Jephthah wrote:

Hi!


I'm simulating a protein conjugate and thus uses custom residues. Is
there
any way to make the dssp program aware of the custom residues (and does
it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.


If you've got custom residues as integral parts of the protein, they

need
to be defined as such in residuetypes.dat, or otherwise defined in a
suitable custom index group.  Presumably you have to have done one or the
other before running the simulation.  If the custom residues have normal
amino acid backbone features, doing DSSP analysis makes sense.  If
something is failing, run dssp directly, not via do_dssp, to determine if
the failure is within dssp or do_dssp.

-Justin

--
==

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

==

--
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

==
--
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

==
--
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.

Re: [gmx-users] DSSP with gmx 5.0.4

[Mark Abraham]

On 03/04/2015 7:36 am, "RJ"  wrote:
>
> Dear gmx users,
>
>
> I tried DSSP of both binary and .exe by renaming it as dssp
(dssp-2.0.4-linux-amd64 & dssp-2.0.4-win32.exe from
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in
usr/local/bin/dssp.

Don't try to install a Windows program. Remove everything and then use only
the Linux version that matches your system.

>
> set the excusable too (  "which dssp" /usr/local/bin/dssp).
>
>
> Both of them gives  same error as follows;
> I also given a permission for dssp file "chmod 777 dssp" but still the
error doesnt go. I use all new version but cant fix it? Any help plz.

That command can only work if you are in the same directory, and as root.
You didn't specify anything about that, so probably the dash binary has the
wrong permissions. Inspect them with ls -l.

Mark

>
> gmx do_dssp -f prd_noPBC.xtc -s prd.tpr -sc scount.xvg -o ss.xpm -dt 10
-ver 2
>
>
> Selected 5: 'MainChain'
> There are 1446 residues in your selected group
> dssp cmd='/usr/local/bin/dssp -i ddiyE5RC -o ddPnxMzu > /dev/null 2>
/dev/null'
> Reading frame   0 time0.000
> Back Off! I just backed up ddiyE5RC to ./#ddiyE5RC.1#
>
>
> ---
> Program gmx, VERSION 5.0.4
> Source code file:
/home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
option.
> ---
> Program gmx, VERSION 5.0.4
> Source code file:
/home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
option.
>
>
>
> --
> 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.
-- 
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.

Re: [gmx-users] dssp installation using cygwin

[Mark Abraham]

Hi,

Same as with UNIX. Download the windows binary and teach gmx do_dssp where
it is.

Mark

On Mon, Jun 26, 2017 at 10:26 AM Neha Gupta  wrote:

> Hi gromacs users,
>
>  I am using gromacs in windows  through cygwin
>
> How to install dssp through cygwin?
>
> Can anyone help?
>
> Thanks,
> Neha
> --
> 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.
>
-- 
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.

Re: [gmx-users] DSSP graph re-scale

[Mohammadreza Niknam Hamidabad]

Dear Syah,

the answer depends on the way you're creating .eps file. I'm assuming that
you're using the gmx do_dssp then gmx xpm2ps.
something like this can be used:

gmx do_dssp -f final.xtc -s my.tpr -n new.ndx -map first.map -tu ns -b 700
-e 1000 -o protein.xpm

gmx xpm2ps -f protein.xpm -di scale.m2p -title top -bx 8.0 -by 50 -o
sec_struc_new.eps

if the x-axis ticks is the problem, you can change the font or anything
related to it, in the .m2p file. (
http://manual.gromacs.org/archive/5.0.3/online/m2p.html)
I hope you find it useful.

Best regards,
Mohammadreza Niknam Hamidabad


On Tue, Sep 10, 2019 at 6:18 AM SGR160055 Student 
wrote:

> Dear experts,
>
> I have an issue to re-scale the x-axis on DSSP graph eps format for my 100
> ns simulation time.
>
> The x-axis of the graph became too compact until it can't be read clearly.
>
> How should I solve this? Is there anyway to re-scale the graph for eps
> format.
>
> Your help is much appreciated. Thank you.
>
>
>
> Regards,
> Syah
> --
> 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.
>
-- 
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.

[gmx-users] dssp version of gromacs 2019.3

[Iman Katouzian]

Good day,
I have downloaded the latest version of DSSP from the site :
https://swift.cmbi.umcn.nl/gv/dssp/

however
as I downloaded and extract the package I see it is named hssp 1.3.4 and
the codes are different from dssp that determines the secondary structures
in gromacs using gmx do_dssp!
can somebody help me on this issue and send me the latest version of DSSP
for gromacs 2019.3 so that I can make it executable and do my task. As I
run it with older version of dssp it reads the code and starts reading the
frames, however even after 2 hours nothing happens and the frame is still
zero!
Many thanks

-- 

*Iman Katouzian*

*Ph.D.** candidate of Food Process Engineering*

*Faculty of Food Science and Technology*

*University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
-- 
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.

[gmx-users] dssp on results of HREX simulation

[Shyno Mathew]

Dear all,

I am getting errors while using do_dssp. I am able to select the main chain
for analysis.

Following is the error I am getting:











*There are 120 residues in your selected groupdssp
cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
/dev/null'Reading frame   0 time 5000.000   Back Off! I just backed up
dd7XLZVM to
./#dd7XLZVM.1#---Program
do_dssp_mpi, VERSION 4.6.7Source code file:
/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
line: 669Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.*


Here is the location of DSSP:
/vega/cheme/users/sm3334/DSSP

As mentioned in the gromacs website/mailing list, I included the path in
the .bashrc file
I tried all the following options, but I am still getting error:

export DSSP=/vega/cheme/users/sm3334/DSSP
export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs
-4.6.7/src/tools/do_dssp.c
export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi

Sincerely,
Shyno

-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University
-- 
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.

Re: [gmx-users] dssp on results of HREX simulation

[Shyno Mathew]

Dear all,


wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
/vega/cheme/users/sm3334/DSSP/dssp

chmod a+x /vega/cheme/users/sm3334/DSSP/dssp

Modify the .bashrc file
export DSSP=/vega/cheme/users/sm3334/DSSP/dssp

*Now I have a question regarding the secondary structure plot. *
How can I make sure the plots shows the maximum x value, y value completely?
Please view the plot here:
https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing

Following are the contents of the .m2p file:
black&white  = no   ; Obsolete
titlefont= Times-Roman  ; A PostScript Font
titlefontsize= 300  ; Font size (pt)
legend   = yes  ; Show the legend
legendfont   = Times-Roman  ; A PostScript Font
legendfontsize   = 250  ; Font size (pt)
xbox = 1.0  ; x-size of a matrix element
ybox = 20.0 ; y-size of a matrix element
matrixspacing= 30.0 ; Space between 2 matrices
xoffset  = 0.0  ; Between matrix and bounding box
yoffset  = 0.0  ; Between matrix and bounding box
x-major  = 1000 ; Major ticks on x axis every ..
frames
x-minor  = 500  ; Id. Minor ticks
x-firstmajor = 5000 ; First frame for major tick
x-majorat0   = no   ; Major tick at first frame
x-majorticklen   = 40.0  ; x-majorticklength
x-minorticklen   = 20.0  ; x-minorticklength
x-label  =  ; Used when there is none in the
.xpm
x-fontsize   = 250  ; Font size (pt)
x-font   = Times-Roman  ; A PostScript Font
x-tickfontsize   = 200  ; Font size (pt)
x-tickfont   = Helvetica; A PostScript Font
y-major  = 20
y-minor  = 10
y-firstmajor = 0
y-majorat0   = no
y-majorticklen   = 40.0
y-minorticklen   = 20.0
y-label  =
y-fontsize   = 250
y-font   = Times-Roman
y-tickfontsize   = 200
y-tickfont   = Helvetica

thanks,
Shyno

On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew  wrote:

> Dear all,
>
> I am getting errors while using do_dssp. I am able to select the main
> chain for analysis.
>
> Following is the error I am getting:
>
>
>
>
>
>
>
>
>
>
>
> *There are 120 residues in your selected groupdssp
> cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
> /dev/null'Reading frame   0 time 5000.000   Back Off! I just backed up
> dd7XLZVM to
> ./#dd7XLZVM.1#---Program
> do_dssp_mpi, VERSION 4.6.7Source code file:
> /vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
> line: 669Fatal error:Failed to execute command: Try specifying your dssp
> version with the -ver option.*
>
>
> Here is the location of DSSP:
> /vega/cheme/users/sm3334/DSSP
>
> As mentioned in the gromacs website/mailing list, I included the path in
> the .bashrc file
> I tried all the following options, but I am still getting error:
>
> export DSSP=/vega/cheme/users/sm3334/DSSP
> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs
> -4.6.7/src/tools/do_dssp.c
> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
> DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
>
> Sincerely,
> Shyno
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>



-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University

On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew  wrote:

> Dear all,
>
> I am getting errors while using do_dssp. I am able to select the main
> chain for analysis.
>
> Following is the error I am getting:
>
>
>
>
>
>
>
>
>
>
>
> *There are 120 residues in your selected groupdssp
> cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
> /dev/null'Reading frame   0 time 5000.000   Back Off! I just backed up
> dd7XLZVM to
> ./#dd7XLZVM.1#---Program
> do_dssp_mpi, VERSION 4.6.7Source code file:
> /vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
> line: 669Fatal error:Failed to execute command: Try specifying your dssp
> version with the -ver option.*
>
>
> Here is the location of DSSP:
> /vega/cheme/users/sm3334/DSSP
>
> As mentioned in the gromacs website/mailing list, I included the path in
> the .bashrc file
> I tried all the following options, but I am still getting error:
>
> ex

Re: [gmx-users] dssp on results of HREX simulation

[Shyno Mathew]

Dear all,


*I was able to fix the error mentioned in the previous message. Here is
what I did:*

wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
/vega/cheme/users/sm3334/DSSP/dssp


chmod a+x /vega/cheme/users/sm3334/DSSP/dssp

Modify the .bashrc file
export DSSP=/vega/cheme/users/sm3334/DSSP/dssp

*Now I have a question regarding the secondary structure plot. *
How can I make sure the plots shows the maximum x value, y value completely?

Please view the plot here:

https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing



Following are the contents of the .m2p file:
black&white  = no   ; Obsolete
titlefont= Times-Roman  ; A PostScript Font
titlefontsize= 300  ; Font size (pt)
legend   = yes  ; Show the legend
legendfont   = Times-Roman  ; A PostScript Font
legendfontsize   = 250  ; Font size (pt)
xbox = 1.0  ; x-size of a matrix element
ybox = 20.0 ; y-size of a matrix element
matrixspacing= 30.0 ; Space between 2 matrices
xoffset  = 0.0  ; Between matrix and bounding box
yoffset  = 0.0  ; Between matrix and bounding box
x-major  = 1000 ; Major ticks on x axis every ..
frames
x-minor  = 500  ; Id. Minor ticks
x-firstmajor = 5000 ; First frame for major tick
x-majorat0   = no   ; Major tick at first frame
x-majorticklen   = 40.0  ; x-majorticklength
x-minorticklen   = 20.0  ; x-minorticklength
x-label  =  ; Used when there is none in the
.xpm
x-fontsize   = 250  ; Font size (pt)
x-font   = Times-Roman  ; A PostScript Font
x-tickfontsize   = 200  ; Font size (pt)
x-tickfont   = Helvetica; A PostScript Font
y-major  = 20
y-minor  = 10
y-firstmajor = 0
y-majorat0   = no
y-majorticklen   = 40.0
y-minorticklen   = 20.0
y-label  =
y-fontsize   = 250
y-font   = Times-Roman
y-tickfontsize   = 200
y-tickfont   = Helvetica

thanks,

Shyno



On Sat, Oct 3, 2015 at 8:48 PM, Shyno Mathew  wrote:

> Dear all,
>
>
> wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
> /vega/cheme/users/sm3334/DSSP/dssp
>
> chmod a+x /vega/cheme/users/sm3334/DSSP/dssp
>
> Modify the .bashrc file
> export DSSP=/vega/cheme/users/sm3334/DSSP/dssp
>
> *Now I have a question regarding the secondary structure plot. *
> How can I make sure the plots shows the maximum x value, y value
> completely?
> Please view the plot here:
>
> https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing
>
>
> Following are the contents of the .m2p file:
> black&white  = no   ; Obsolete
> titlefont= Times-Roman  ; A PostScript Font
> titlefontsize= 300  ; Font size (pt)
> legend   = yes  ; Show the legend
> legendfont   = Times-Roman  ; A PostScript Font
> legendfontsize   = 250  ; Font size (pt)
> xbox = 1.0  ; x-size of a matrix element
> ybox = 20.0 ; y-size of a matrix element
> matrixspacing= 30.0 ; Space between 2 matrices
> xoffset  = 0.0  ; Between matrix and bounding box
> yoffset  = 0.0  ; Between matrix and bounding box
> x-major  = 1000 ; Major ticks on x axis every ..
> frames
> x-minor  = 500  ; Id. Minor ticks
> x-firstmajor = 5000 ; First frame for major tick
> x-majorat0   = no   ; Major tick at first frame
> x-majorticklen   = 40.0  ; x-majorticklength
> x-minorticklen   = 20.0  ; x-minorticklength
> x-label  =  ; Used when there is none in the
> .xpm
> x-fontsize   = 250  ; Font size (pt)
> x-font   = Times-Roman  ; A PostScript Font
> x-tickfontsize   = 200  ; Font size (pt)
> x-tickfont   = Helvetica; A PostScript Font
> y-major  = 20
> y-minor  = 10
> y-firstmajor = 0
> y-majorat0   = no
> y-majorticklen   = 40.0
> y-minorticklen   = 20.0
> y-label  =
> y-fontsize   = 250
> y-font   = Times-Roman
> y-tickfontsize   = 200
> y-tickfont   = Helvetica
>
> thanks,
> Shyno
>
> On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew  wrote:
>
>> Dear all,
>>
>> I am getting errors while using do_dssp. I am able to select the main
>