Re: [gmx-users] Installing DSSP

[Mark Abraham]

Hi,

Start with
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-do_dssp.html

Mark

On Tue, Feb 27, 2018 at 1:00 PM Neha Gupta  wrote:

> Hi,
>
> I use gromacs version 5.1.4 through cygwin
>
> Please let me know how to install DSSP?
>
> Which version of DSSP would be compatible with the above version of
> gromacs?
>
> Thanks,
> Neha
> --
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[gmx-users] Installing DSSP

[Neha Gupta]

Hi,

I use gromacs version 5.1.4 through cygwin

Please let me know how to install DSSP?

Which version of DSSP would be compatible with the above version of gromacs?

Thanks,
Neha
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Re: [gmx-users] Installing DSSP

[Erik Marklund]

Dear Soumadwip,

This is not a problem with do_dssp, but with your deep installation. My guess 
is that you have not completed the installation of dssp.

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se

On 3 Feb 2017, at 07:51, soumadwip ghosh 
> wrote:

Hello all,

I am trying to install dssp in centos 7 for determining the secondary
structure of a protein in combination with do_dssp. These are the steps I
followed:

1. installation directory : /opt/apps/dssp/dssp-2.2.1/

2. but there is no dssp executable in the dssp-2.2.1 directory

3. however there was a dssp.o file in the obj directory of dssp-2.2.1

4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1 directory

5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/

6. export dssp=/usr/local/bin/dssp



but inspite of executing the above steps, when we run the do_dssp command we get
the following error : Fatal error: DSSP executable
(usr/local/bin/dssp/dssp) does
not exist (use setenv DSSP)

PS. we are using bash


I have read various threads on the errors related to do_dssp but could
not find a solution.

Any kind of help would be appreciated.


Best,

Soumadwip Ghosh

Research Associate

Indian Institute of Technology Bombay

India
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Re: [gmx-users] Installing DSSP

[masoud keramati]

Hi

follow these steps:

1)sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.2.1-linux-i386 -O
/usr/local/bin/dssp

2)sudo chmod a+x /usr/local/bin/dssp

3)export DSSP=/usr/local/bin/dssp

On Fri, Feb 3, 2017 at 3:15 PM, Mark Abraham 
wrote:

> Hi,
>
> On Fri, Feb 3, 2017 at 7:52 AM soumadwip ghosh 
> wrote:
>
> > Hello all,
> >
> > I am trying to install dssp in centos 7 for determining the secondary
> > structure of a protein in combination with do_dssp. These are the steps I
> > followed:
> >
> > 1. installation directory : /opt/apps/dssp/dssp-2.2.1/
> >
> > 2. but there is no dssp executable in the dssp-2.2.1 directory
> >
> > 3. however there was a dssp.o file in the obj directory of dssp-2.2.1
> >
> > 4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1
> directory
> >
>
> That cannot possibly work. Please make sure you are following the dssp
> installation instructions.
>
> Mark
>
>
> > 5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/
> >
> > 6. export dssp=/usr/local/bin/dssp
> >
> >
> >
> > but inspite of executing the above steps, when we run the do_dssp command
> > we get
> > the following error : Fatal error: DSSP executable
> > (usr/local/bin/dssp/dssp) does
> > not exist (use setenv DSSP)
> >
> > PS. we are using bash
> >
> >
> > I have read various threads on the errors related to do_dssp but could
> > not find a solution.
> >
> > Any kind of help would be appreciated.
> >
> >
> > Best,
> >
> > Soumadwip Ghosh
> >
> > Research Associate
> >
> > Indian Institute of Technology Bombay
> >
> > India
> > --
> > 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.
> >
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>
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Re: [gmx-users] Installing DSSP

[Mark Abraham]

Hi,

On Fri, Feb 3, 2017 at 7:52 AM soumadwip ghosh 
wrote:

> Hello all,
>
> I am trying to install dssp in centos 7 for determining the secondary
> structure of a protein in combination with do_dssp. These are the steps I
> followed:
>
> 1. installation directory : /opt/apps/dssp/dssp-2.2.1/
>
> 2. but there is no dssp executable in the dssp-2.2.1 directory
>
> 3. however there was a dssp.o file in the obj directory of dssp-2.2.1
>
> 4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1 directory
>

That cannot possibly work. Please make sure you are following the dssp
installation instructions.

Mark


> 5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/
>
> 6. export dssp=/usr/local/bin/dssp
>
>
>
> but inspite of executing the above steps, when we run the do_dssp command
> we get
> the following error : Fatal error: DSSP executable
> (usr/local/bin/dssp/dssp) does
> not exist (use setenv DSSP)
>
> PS. we are using bash
>
>
> I have read various threads on the errors related to do_dssp but could
> not find a solution.
>
> Any kind of help would be appreciated.
>
>
> Best,
>
> Soumadwip Ghosh
>
> Research Associate
>
> Indian Institute of Technology Bombay
>
> India
> --
> 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.
>
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[gmx-users] Installing DSSP

[soumadwip ghosh]

Hello all,

I am trying to install dssp in centos 7 for determining the secondary
structure of a protein in combination with do_dssp. These are the steps I
followed:

1. installation directory : /opt/apps/dssp/dssp-2.2.1/

2. but there is no dssp executable in the dssp-2.2.1 directory

3. however there was a dssp.o file in the obj directory of dssp-2.2.1

4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1 directory

5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/

6. export dssp=/usr/local/bin/dssp



but inspite of executing the above steps, when we run the do_dssp command we get
the following error : Fatal error: DSSP executable
(usr/local/bin/dssp/dssp) does
not exist (use setenv DSSP)

PS. we are using bash


I have read various threads on the errors related to do_dssp but could
not find a solution.

Any kind of help would be appreciated.


Best,

Soumadwip Ghosh

Research Associate

Indian Institute of Technology Bombay

India
-- 
Gromacs Users mailing list

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