[gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Nikunj Maheshwari
Dear all,

I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp command but get the following error each
time:

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 
/dev/null 2 /dev/null


Is there any way to rectify it?

Thanks.
Nikunj
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Erik Marklund
Hi,

Search the mailing list. This problem and its solution has been repeatedly 
discussed.

Erik

On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:

 Dear all,
 
 I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
 I am trying to use it for do_dssp command but get the following error each
 time:
 
 Fatal error:
 Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 
 /dev/null 2 /dev/null
 
 
 Is there any way to rectify it?
 
 Thanks.
 Nikunj
 -- 
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Nikunj Maheshwari
Yes I did searched. But for most people, there were issues regarding the
path or wrong DSSP.
DSSP runs for me, but do_dssp does not.


On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote:

 Hi,

 Search the mailing list. This problem and its solution has been repeatedly
 discussed.

 Erik

 On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:

  Dear all,
 
  I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
  I am trying to use it for do_dssp command but get the following error
 each
  time:
 
  Fatal error:
  Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 
  /dev/null 2 /dev/null
  
 
  Is there any way to rectify it?
 
  Thanks.
  Nikunj
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Mark Abraham
Right. And what is its location?
On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:

 Yes I did searched. But for most people, there were issues regarding the
 path or wrong DSSP.
 DSSP runs for me, but do_dssp does not.


 On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se
 wrote:

  Hi,
 
  Search the mailing list. This problem and its solution has been
 repeatedly
  discussed.
 
  Erik
 
  On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com
  wrote:
 
   Dear all,
  
   I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
   I am trying to use it for do_dssp command but get the following error
  each
   time:
  
   Fatal error:
   Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 
   /dev/null 2 /dev/null
   
  
   Is there any way to rectify it?
  
   Thanks.
   Nikunj
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Nikunj Maheshwari
The location of dssp is /usr/local/bin/dssp


On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 Right. And what is its location?
 On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:

  Yes I did searched. But for most people, there were issues regarding the
  path or wrong DSSP.
  DSSP runs for me, but do_dssp does not.
 
 
  On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se
  wrote:
 
   Hi,
  
   Search the mailing list. This problem and its solution has been
  repeatedly
   discussed.
  
   Erik
  
   On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com
   wrote:
  
Dear all,
   
I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp command but get the following error
   each
time:
   
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68
 
/dev/null 2 /dev/null

   
Is there any way to rectify it?
   
Thanks.
Nikunj
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Erik Marklund
Search again. The syntax for invoking dssp changed at some point and it took a 
while before do_dssp adapted to that. If your do_dssp is lacking the -ver 
option then I'm quite confident that it uses the old syntax, which doesn't work 
with the newer versions (v. 2.0+ I think) of dssp.

Erik
 
On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:

 Yes I did searched. But for most people, there were issues regarding the
 path or wrong DSSP.
 DSSP runs for me, but do_dssp does not.
 
 
 On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
 
 Hi,
 
 Search the mailing list. This problem and its solution has been repeatedly
 discussed.
 
 Erik
 
 On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:
 
 Dear all,
 
 I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
 I am trying to use it for do_dssp command but get the following error
 each
 time:
 
 Fatal error:
 Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 
 /dev/null 2 /dev/null
 
 
 Is there any way to rectify it?
 
 Thanks.
 Nikunj
 --
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Nikunj Maheshwari
Yes I checked. do_dssp has no -ver option.
I also found out this link

https://gerrit.gromacs.org/#/c/687/

but dont know how to install/use it.

Or maybe I can install DsspOld and see?



On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote:

 Search again. The syntax for invoking dssp changed at some point and it
 took a while before do_dssp adapted to that. If your do_dssp is lacking the
 -ver option then I'm quite confident that it uses the old syntax, which
 doesn't work with the newer versions (v. 2.0+ I think) of dssp.

 Erik

 On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:

  Yes I did searched. But for most people, there were issues regarding the
  path or wrong DSSP.
  DSSP runs for me, but do_dssp does not.
 
 
  On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se
 wrote:
 
  Hi,
 
  Search the mailing list. This problem and its solution has been
 repeatedly
  discussed.
 
  Erik
 
  On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com
  wrote:
 
  Dear all,
 
  I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
  I am trying to use it for do_dssp command but get the following error
  each
  time:
 
  Fatal error:
  Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 
  /dev/null 2 /dev/null
  
 
  Is there any way to rectify it?
 
  Thanks.
  Nikunj
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Erik Marklund
You have (at least) two easy options.

1) Install old_dssp that is available through the dssp web page.  
2) Install a newer version of gromacs than you have at the moment. What version 
do you currently use?

Erik

On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:

 Yes I checked. do_dssp has no -ver option.
 I also found out this link
 
 https://gerrit.gromacs.org/#/c/687/
 
 but dont know how to install/use it.
 
 Or maybe I can install DsspOld and see?
 
 
 
 On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
 
 Search again. The syntax for invoking dssp changed at some point and it
 took a while before do_dssp adapted to that. If your do_dssp is lacking the
 -ver option then I'm quite confident that it uses the old syntax, which
 doesn't work with the newer versions (v. 2.0+ I think) of dssp.
 
 Erik
 
 On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:
 
 Yes I did searched. But for most people, there were issues regarding the
 path or wrong DSSP.
 DSSP runs for me, but do_dssp does not.
 
 
 On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se
 wrote:
 
 Hi,
 
 Search the mailing list. This problem and its solution has been
 repeatedly
 discussed.
 
 Erik
 
 On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:
 
 Dear all,
 
 I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
 I am trying to use it for do_dssp command but get the following error
 each
 time:
 
 Fatal error:
 Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 
 /dev/null 2 /dev/null
 
 
 Is there any way to rectify it?
 
 Thanks.
 Nikunj
 --
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Re: [gmx-users] dssp works fine, but do_dssp gives fatal error

2013-06-12 Thread Nikunj Maheshwari
My current Gromacs version is 4.5.5
I think using the first option will be easy and quick.


On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund er...@xray.bmc.uu.se wrote:

 You have (at least) two easy options.

 1) Install old_dssp that is available through the dssp web page.
 2) Install a newer version of gromacs than you have at the moment. What
 version do you currently use?

 Erik

 On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com
 wrote:

  Yes I checked. do_dssp has no -ver option.
  I also found out this link
 
  https://gerrit.gromacs.org/#/c/687/
 
  but dont know how to install/use it.
 
  Or maybe I can install DsspOld and see?
 
 
 
  On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se
 wrote:
 
  Search again. The syntax for invoking dssp changed at some point and it
  took a while before do_dssp adapted to that. If your do_dssp is lacking
 the
  -ver option then I'm quite confident that it uses the old syntax, which
  doesn't work with the newer versions (v. 2.0+ I think) of dssp.
 
  Erik
 
  On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com
  wrote:
 
  Yes I did searched. But for most people, there were issues regarding
 the
  path or wrong DSSP.
  DSSP runs for me, but do_dssp does not.
 
 
  On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se
  wrote:
 
  Hi,
 
  Search the mailing list. This problem and its solution has been
  repeatedly
  discussed.
 
  Erik
 
  On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com
 
  wrote:
 
  Dear all,
 
  I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
  I am trying to use it for do_dssp command but get the following error
  each
  time:
 
  Fatal error:
  Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68
 
  /dev/null 2 /dev/null
  
 
  Is there any way to rectify it?
 
  Thanks.
  Nikunj
  --
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
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