Re: [gmx-users] do_dssp

[Justin Lemkul]

On 5/14/13 11:11 AM, Xu Dong Huang wrote:

Preeti,

if do_dssp doesn't work for you, try to do it manually using the following web 
service:
http://www.cmbi.ru.nl/hsspsoap/

I use it because my platform (MAC OSX) can't run DO_DSSP



I've used dssp/do_dssp on Mac for years.  It's all a matter of getting the right 
binary or installing from source.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[Xu Dong Huang]

Preeti,

if do_dssp doesn't work for you, try to do it manually using the following web 
service: 
http://www.cmbi.ru.nl/hsspsoap/

I use it because my platform (MAC OSX) can't run DO_DSSP

Best of luck!


On May 14, 2013, at 11:00 AM, Preeti Choudhary 
 wrote:

> I am facing problem while using do_dssp.I
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[gmx-users] do_dssp

[Preeti Choudhary]

I am facing problem while using do_dssp.I
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Re: [gmx-users] do_dssp

[Erik Marklund]

Hi,

I'll try out the 2.1.0 with do_dssp and see if there's something  
problematic with this new version. Good thing you brought it up.


Erik

On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote:


Hi Erik,

Since I read in the mailing list that nobody had asked about 2.1.0,  
just
decided to try an older version before going into the trouble  
itself...

Kind of coward, I know, but the troubles with that version are already
reported so that  I thought things would be easier :)
Thank-you a lot for your comments



2013/3/1 Erik Marklund 


Interesting. Perhaps there are new issues with 2.1.0. Did you try to
execute the command yourself?

Erik


On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:

The issue I mentioned was with dssp-2.1.0.  I changed to 2.0.1 and it

works
fine. However, when converting the xpm to eps I get I plot very  
small,
where one barely can see the colour code and the legend is sooo  
big. Does

anyone know how to change that?





2013/3/1 Erik Marklund 

What happens if you execute the command (/usr/local/bin/dssp/ -i  
ddQ3PqtX

-o ddR1HavD) in your terminal?


Erik

On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:

I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error  
you

got:



dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/ 
null 2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

---
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/
src/tools/gmx_do_dssp.c,

line:
667

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

-ver
option.

How can I fix that?

Thanks







2013/1/15 James Starlight 

Justin, thanks both options works perfect.




James

2013/1/15 Justin Lemkul :




On 1/15/13 7:13 AM, James Starlight wrote:



Justin,


I  want to obtain timescale on X as well as number of  
residues on Y
on the xmp graph . By  default that graph has not legend so  
it's hard

to analyse it .


The legends are printed in the .xvg header.  I've never had a

problem
plotting its contents (though they are usually somewhat  
unclear when


plotted


together) with xmgrace -nxy scount.xvg



By the way have you forced with some problems with dppc ?  
Simetimes



I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/ 
null 2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


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

-ver option.

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3


Since dssp changed its command line options, Gromacs had to  
adapt as


well.


The error tells you to use the -ver option; you should do so.

Version 2
should be the default, so check to make sure you're actually  
using

that
version and not the old dssp.


-Justin

--
====


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 
>




====

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Re: [gmx-users] do_dssp

[Miguel Ángel Mompeán García]

Hi Erik,

Since I read in the mailing list that nobody had asked about 2.1.0, just
decided to try an older version before going into the trouble itself...
Kind of coward, I know, but the troubles with that version are already
reported so that  I thought things would be easier :)
Thank-you a lot for your comments



2013/3/1 Erik Marklund 

> Interesting. Perhaps there are new issues with 2.1.0. Did you try to
> execute the command yourself?
>
> Erik
>
>
> On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:
>
>  The issue I mentioned was with dssp-2.1.0.  I changed to 2.0.1 and it
>> works
>> fine. However, when converting the xpm to eps I get I plot very small,
>> where one barely can see the colour code and the legend is sooo big. Does
>> anyone know how to change that?
>>
>>
>>
>>
>>
>> 2013/3/1 Erik Marklund 
>>
>>  What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX
>>> -o ddR1HavD) in your terminal?
>>>
>>>
>>> Erik
>>>
>>> On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
>>>
>>> I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you
>>> got:
>>>

 dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
 /dev/null'
 Reading frame   0 time0.000
 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

 ---
 Program do_dssp, VERSION 4.6
 Source code file: /usr/local/bin/gromacs-4.6/
 src/tools/gmx_do_dssp.c,

 line:
 667

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

 How can I fix that?

 Thanks







 2013/1/15 James Starlight 

 Justin, thanks both options works perfect.

>
>
> James
>
> 2013/1/15 Justin Lemkul :
>
>
>>
>> On 1/15/13 7:13 AM, James Starlight wrote:
>>
>>
>>> Justin,
>>>
>>>
>>> I  want to obtain timescale on X as well as number of residues on Y
>>> on the xmp graph . By  default that graph has not legend so it's hard
>>> to analyse it .
>>>
>>>
>>>  The legends are printed in the .xvg header.  I've never had a
>> problem
>> plotting its contents (though they are usually somewhat unclear when
>>
>>  plotted
>
>  together) with xmgrace -nxy scount.xvg
>>
>>
>> By the way have you forced with some problems with dppc ? Simetimes
>>
>>> I've obtain error like
>>>
>>>
>>> There are 286 residues in your selected group
>>> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2>
>>> /dev/null'
>>> Reading frame   0 time0.000
>>> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1
>>>
>>>
>>> Fatal error:
>>> Failed to execute command: Try specifying your dssp version with the
>>> -ver option.
>>>
>>> and I dont know how to fix it.
>>>
>>> I'm using gromacs-4.6-beta 3 with dssp 2.0.3
>>>
>>>
>>>  Since dssp changed its command line options, Gromacs had to adapt as
>>
>>  well.
>
>  The error tells you to use the -ver option; you should do so.
>>  Version 2
>> should be the default, so check to make sure you're actually using
>> that
>> version and not the old dssp.
>>
>>
>> -Justin
>>
>> --
>> ====
>>
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>> ====
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search
>> http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>> posting!
>>
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>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/Support/Mailing_Lists
>> 
>> >
>>
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Re: [gmx-users] do_dssp

[Erik Marklund]

Interesting. Perhaps there are new issues with 2.1.0. Did you try to  
execute the command yourself?


Erik

On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:

The issue I mentioned was with dssp-2.1.0.  I changed to 2.0.1 and  
it works

fine. However, when converting the xpm to eps I get I plot very small,
where one barely can see the colour code and the legend is sooo big.  
Does

anyone know how to change that?





2013/3/1 Erik Marklund 

What happens if you execute the command (/usr/local/bin/dssp/ -i  
ddQ3PqtX

-o ddR1HavD) in your terminal?


Erik

On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:

I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error  
you got:


dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null  
2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

--**-
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/**src/tools/ 
gmx_do_dssp.c,

line:
667

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

option.

How can I fix that?

Thanks







2013/1/15 James Starlight 

Justin, thanks both options works perfect.



James

2013/1/15 Justin Lemkul :




On 1/15/13 7:13 AM, James Starlight wrote:



Justin,


I  want to obtain timescale on X as well as number of residues  
on Y
on the xmp graph . By  default that graph has not legend so  
it's hard

to analyse it .


The legends are printed in the .xvg header.  I've never had a  
problem
plotting its contents (though they are usually somewhat unclear  
when



plotted


together) with xmgrace -nxy scount.xvg


By the way have you forced with some problems with dppc ?  
Simetimes

I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/ 
null 2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


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

-ver option.

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3


Since dssp changed its command line options, Gromacs had to  
adapt as



well.

The error tells you to use the -ver option; you should do so.   
Version 2
should be the default, so check to make sure you're actually  
using that

version and not the old dssp.


-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin


==**==
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Re: [gmx-users] do_dssp

[Justin Lemkul]

On 3/1/13 11:16 AM, Miguel Ángel Mompeán García wrote:

The issue I mentioned was with dssp-2.1.0.  I changed to 2.0.1 and it works
fine. However, when converting the xpm to eps I get I plot very small,
where one barely can see the colour code and the legend is sooo big. Does
anyone know how to change that?



Supply an .m2p file to xpm2ps -di to adjust the size of each matrix element. 
There is an example in the online manual.


-Justin






2013/3/1 Erik Marklund 


What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX
-o ddR1HavD) in your terminal?


Erik

On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:

  I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:


dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

--**-
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/**src/tools/gmx_do_dssp.c,
line:
667

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

How can I fix that?

Thanks







2013/1/15 James Starlight 

  Justin, thanks both options works perfect.



James

2013/1/15 Justin Lemkul :




On 1/15/13 7:13 AM, James Starlight wrote:



Justin,


  I  want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By  default that graph has not legend so it's hard
to analyse it .



The legends are printed in the .xvg header.  I've never had a problem
plotting its contents (though they are usually somewhat unclear when


plotted


together) with xmgrace -nxy scount.xvg


  By the way have you forced with some problems with dppc ? Simetimes

I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2>
/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


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

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3



Since dssp changed its command line options, Gromacs had to adapt as


well.


The error tells you to use the -ver option; you should do so.  Version 2
should be the default, so check to make sure you're actually using that
version and not the old dssp.


-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

==**==
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 posting!
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Re: [gmx-users] do_dssp

[Miguel Ángel Mompeán García]

The issue I mentioned was with dssp-2.1.0.  I changed to 2.0.1 and it works
fine. However, when converting the xpm to eps I get I plot very small,
where one barely can see the colour code and the legend is sooo big. Does
anyone know how to change that?





2013/3/1 Erik Marklund 

> What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX
> -o ddR1HavD) in your terminal?
>
>
> Erik
>
> On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
>
>  I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:
>>
>> dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
>> /dev/null'
>> Reading frame   0 time0.000
>> Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#
>>
>> --**-
>> Program do_dssp, VERSION 4.6
>> Source code file: /usr/local/bin/gromacs-4.6/**src/tools/gmx_do_dssp.c,
>> line:
>> 667
>>
>> Fatal error:
>> Failed to execute command: Try specifying your dssp version with the -ver
>> option.
>>
>> How can I fix that?
>>
>> Thanks
>>
>>
>>
>>
>>
>>
>>
>> 2013/1/15 James Starlight 
>>
>>  Justin, thanks both options works perfect.
>>>
>>>
>>> James
>>>
>>> 2013/1/15 Justin Lemkul :
>>>


 On 1/15/13 7:13 AM, James Starlight wrote:

>
> Justin,
>
>
>  I  want to obtain timescale on X as well as number of residues on Y
> on the xmp graph . By  default that graph has not legend so it's hard
> to analyse it .
>
>
 The legends are printed in the .xvg header.  I've never had a problem
 plotting its contents (though they are usually somewhat unclear when

>>> plotted
>>>
 together) with xmgrace -nxy scount.xvg


  By the way have you forced with some problems with dppc ? Simetimes
> I've obtain error like
>
>
> There are 286 residues in your selected group
> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2>
> /dev/null'
> Reading frame   0 time0.000
> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the
> -ver option.
>
> and I dont know how to fix it.
>
> I'm using gromacs-4.6-beta 3 with dssp 2.0.3
>
>
 Since dssp changed its command line options, Gromacs had to adapt as

>>> well.
>>>
 The error tells you to use the -ver option; you should do so.  Version 2
 should be the default, so check to make sure you're actually using that
 version and not the old dssp.


 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] do_dssp

[Erik Marklund]

What happens if you execute the command (/usr/local/bin/dssp/ -i  
ddQ3PqtX -o ddR1HavD) in your terminal?


Erik

On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:

I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error  
you got:


dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

---
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/src/tools/ 
gmx_do_dssp.c, line:

667

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

option.

How can I fix that?

Thanks







2013/1/15 James Starlight 


Justin, thanks both options works perfect.


James

2013/1/15 Justin Lemkul :



On 1/15/13 7:13 AM, James Starlight wrote:


Justin,


 I  want to obtain timescale on X as well as number of residues  
on Y
on the xmp graph . By  default that graph has not legend so it's  
hard

to analyse it .



The legends are printed in the .xvg header.  I've never had a  
problem

plotting its contents (though they are usually somewhat unclear when

plotted

together) with xmgrace -nxy scount.xvg



By the way have you forced with some problems with dppc ? Simetimes
I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null  
2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


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

-ver option.

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3



Since dssp changed its command line options, Gromacs had to adapt as

well.
The error tells you to use the -ver option; you should do so.   
Version 2
should be the default, so check to make sure you're actually using  
that

version and not the old dssp.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[Erik Marklund]

With -ver, just like it says. do_dssp -h explains how. What dssp  
version do you have?


Erik

On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:

I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error  
you got:


dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

---
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/src/tools/ 
gmx_do_dssp.c, line:

667

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

option.

How can I fix that?

Thanks







2013/1/15 James Starlight 


Justin, thanks both options works perfect.


James

2013/1/15 Justin Lemkul :



On 1/15/13 7:13 AM, James Starlight wrote:


Justin,


 I  want to obtain timescale on X as well as number of residues  
on Y
on the xmp graph . By  default that graph has not legend so it's  
hard

to analyse it .



The legends are printed in the .xvg header.  I've never had a  
problem

plotting its contents (though they are usually somewhat unclear when

plotted

together) with xmgrace -nxy scount.xvg



By the way have you forced with some problems with dppc ? Simetimes
I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null  
2>

/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


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

-ver option.

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3



Since dssp changed its command line options, Gromacs had to adapt as

well.
The error tells you to use the -ver option; you should do so.   
Version 2
should be the default, so check to make sure you're actually using  
that

version and not the old dssp.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp with 4.6

[Miguel Ángel Mompeán García]

Dear gmx users,

Has anyone tried dssp-2.1.0 with gromacs-4.6?
I am having the common problems that were supossed not to be in the new
releases
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Re: [gmx-users] do_dssp

[Miguel Ángel Mompeán García]

I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:

dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
/dev/null'
Reading frame   0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

---
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/src/tools/gmx_do_dssp.c, line:
667

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

How can I fix that?

Thanks







2013/1/15 James Starlight 

> Justin, thanks both options works perfect.
>
>
> James
>
> 2013/1/15 Justin Lemkul :
> >
> >
> > On 1/15/13 7:13 AM, James Starlight wrote:
> >>
> >> Justin,
> >>
> >>
> >>   I  want to obtain timescale on X as well as number of residues on Y
> >> on the xmp graph . By  default that graph has not legend so it's hard
> >> to analyse it .
> >>
> >
> > The legends are printed in the .xvg header.  I've never had a problem
> > plotting its contents (though they are usually somewhat unclear when
> plotted
> > together) with xmgrace -nxy scount.xvg
> >
> >
> >> By the way have you forced with some problems with dppc ? Simetimes
> >> I've obtain error like
> >>
> >>
> >> There are 286 residues in your selected group
> >> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2>
> >> /dev/null'
> >> Reading frame   0 time0.000
> >> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1
> >>
> >>
> >> Fatal error:
> >> Failed to execute command: Try specifying your dssp version with the
> >> -ver option.
> >>
> >> and I dont know how to fix it.
> >>
> >> I'm using gromacs-4.6-beta 3 with dssp 2.0.3
> >>
> >
> > Since dssp changed its command line options, Gromacs had to adapt as
> well.
> > The error tells you to use the -ver option; you should do so.  Version 2
> > should be the default, so check to make sure you're actually using that
> > version and not the old dssp.
> >
> >
> > -Justin
> >
> > --
> > 
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] do_dssp

[James Starlight]

Justin, thanks both options works perfect.


James

2013/1/15 Justin Lemkul :
>
>
> On 1/15/13 7:13 AM, James Starlight wrote:
>>
>> Justin,
>>
>>
>>   I  want to obtain timescale on X as well as number of residues on Y
>> on the xmp graph . By  default that graph has not legend so it's hard
>> to analyse it .
>>
>
> The legends are printed in the .xvg header.  I've never had a problem
> plotting its contents (though they are usually somewhat unclear when plotted
> together) with xmgrace -nxy scount.xvg
>
>
>> By the way have you forced with some problems with dppc ? Simetimes
>> I've obtain error like
>>
>>
>> There are 286 residues in your selected group
>> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2>
>> /dev/null'
>> Reading frame   0 time0.000
>> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1
>>
>>
>> Fatal error:
>> Failed to execute command: Try specifying your dssp version with the
>> -ver option.
>>
>> and I dont know how to fix it.
>>
>> I'm using gromacs-4.6-beta 3 with dssp 2.0.3
>>
>
> Since dssp changed its command line options, Gromacs had to adapt as well.
> The error tells you to use the -ver option; you should do so.  Version 2
> should be the default, so check to make sure you're actually using that
> version and not the old dssp.
>
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] do_dssp

[Justin Lemkul]

On 1/15/13 7:13 AM, James Starlight wrote:

Justin,


  I  want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By  default that graph has not legend so it's hard
to analyse it .



The legends are printed in the .xvg header.  I've never had a problem plotting 
its contents (though they are usually somewhat unclear when plotted together) 
with xmgrace -nxy scount.xvg



By the way have you forced with some problems with dppc ? Simetimes
I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2> /dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


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

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3



Since dssp changed its command line options, Gromacs had to adapt as well.  The 
error tells you to use the -ver option; you should do so.  Version 2 should be 
the default, so check to make sure you're actually using that version and not 
the old dssp.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[James Starlight]

Justin,


 I  want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By  default that graph has not legend so it's hard
to analyse it .

By the way have you forced with some problems with dppc ? Simetimes
I've obtain error like


There are 286 residues in your selected group
dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2> /dev/null'
Reading frame   0 time0.000
Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1


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

and I dont know how to fix it.

I'm using gromacs-4.6-beta 3 with dssp 2.0.3

James

2013/1/15 Justin Lemkul :
>
>
> On 1/15/13 3:19 AM, James Starlight wrote:
>>
>> Dear Gromacs Users!
>>
>> I'd like to know if it's possible to obtain some values from do_dssp
>> except the graph diagrams of the ss dynamics ? For example I wounder
>> to know values of how many residues were in helix, sheet or coil
>> conformation during my simulation ?
>
>
> That's what scount.xvg contains.
>
>
>> By the way during analysis of the graph obtained from do_dssp produced by
>> do_dssp -s minim -f md_noPBC.xtc -o ./results/dssp
>>
>> I didnt found legend on the x and y (time,  number of residue) as well
>> as color scheme of particular ss element. How I can add it to that
>> graph ?
>>
>
> I don't understand what you're asking here.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] do_dssp

[Justin Lemkul]

On 1/15/13 3:19 AM, James Starlight wrote:

Dear Gromacs Users!

I'd like to know if it's possible to obtain some values from do_dssp
except the graph diagrams of the ss dynamics ? For example I wounder
to know values of how many residues were in helix, sheet or coil
conformation during my simulation ?


That's what scount.xvg contains.


By the way during analysis of the graph obtained from do_dssp produced by
do_dssp -s minim -f md_noPBC.xtc -o ./results/dssp

I didnt found legend on the x and y (time,  number of residue) as well
as color scheme of particular ss element. How I can add it to that
graph ?



I don't understand what you're asking here.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp

[James Starlight]

Dear Gromacs Users!

I'd like to know if it's possible to obtain some values from do_dssp
except the graph diagrams of the ss dynamics ? For example I wounder
to know values of how many residues were in helix, sheet or coil
conformation during my simulation ?
By the way during analysis of the graph obtained from do_dssp produced by
do_dssp -s minim -f md_noPBC.xtc -o ./results/dssp

I didnt found legend on the x and y (time,  number of residue) as well
as color scheme of particular ss element. How I can add it to that
graph ?


Thanks for help,


James
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Re: [gmx-users] do_dssp Segmentation fault

[Erik Marklund]

Hi,

The explanation is that DSSP changed its syntax some time ago and do_dssp no 
longer complied. More recent versions of do_dssp follows the new syntax  while 
still supporting the old one.

Erik

12 nov 2012 kl. 10.55 skrev João Henriques:

> Hello,
> 
> do_dssp (4.5.5) is broken. There are two possible answers you're gonna get
> here:
> 
> 1) Use old dssp, which you are using.
> 2) You're an idiot, which are not.
> 
> What I did to solve the problem was, download gmx from git, and substitute
> the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version.
> Re-compile it and voila! This do_dssp version accepts both old and new dssp
> and you have to specify which version with the flag -ver if I remember
> correctly.
> 
> This worked perfectly for me. I hope it helps you as well.
> 
> All the best,
> João Henriques
> 
> On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986  wrote:
> 
>> Hi all,
>>   I am meeting the following error in Gromacs 4.5.5 with do_dssp
>>   Here is the command
>>   do_dssp -f md.xtc -s md.tpr -o dssp.xpm
>>  give me the following error
>>   segmentation fault
>>  I have downloaded the executable DSSP form
>> http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but
>> do_dssp did not work.
>>  How can I fix it?
>>  Thanks a lot
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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> 
> 
> 
> -- 
> João Henriques
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---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
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Re: [gmx-users] do_dssp Segmentation fault

[João Henriques]

Hello,

do_dssp (4.5.5) is broken. There are two possible answers you're gonna get
here:

1) Use old dssp, which you are using.
2) You're an idiot, which are not.

What I did to solve the problem was, download gmx from git, and substitute
the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version.
Re-compile it and voila! This do_dssp version accepts both old and new dssp
and you have to specify which version with the flag -ver if I remember
correctly.

This worked perfectly for me. I hope it helps you as well.

All the best,
João Henriques

On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986  wrote:

> Hi all,
>I am meeting the following error in Gromacs 4.5.5 with do_dssp
>Here is the command
>do_dssp -f md.xtc -s md.tpr -o dssp.xpm
>   give me the following error
>segmentation fault
>   I have downloaded the executable DSSP form
> http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but
> do_dssp did not work.
>   How can I fix it?
>   Thanks a lot
>
>
>
>
>
>
>
>
>
>
> --
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[gmx-users] do_dssp Segmentation fault

[mshappy1986]

Hi all,
   I am meeting the following error in Gromacs 4.5.5 with do_dssp
   Here is the command
   do_dssp -f md.xtc -s md.tpr -o dssp.xpm  
  give me the following error
   segmentation fault  
  I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ 
and set the environment variable, but do_dssp did not work.
  How can I fix it?
  Thanks a lot






 



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Re: [gmx-users] do_dssp segmental fault

[archana sonawani]

Hi Deb,

I recently installed dssp for Gromacs 4.5.4 on RHEL4

You have to just copy the dsspcmbi downloaded from linux distribution to
/usr/local/bin (No need to set an environment variable DSSP if dspcmbi is
in /usr/loca/bin as it is the default path for gromacs)

Rename the dsspcmbi to dssp

chmod +x dssp is required  if doesn't show as executable. Run do_dssp at
any other location. This worked for me.

Regards,
Archana

On Mon, Aug 20, 2012 at 10:49 AM, Debajyoti Ghosh wrote:

> Dear gmx users,
> I recently upgraded the operating system to Ubuntu 12 and re-installed
> Gromacs 4.5.5. But I could not re-install dssp.
>
> I did the following:
> (1) I downloaded dsspcmbi from http://swift.cmbi.ru.nl/gv/dssp/
> Went to distributions- DSSPold - Linux Distributions to download
> dsspcmbi. (2) Moved to /usr/local/bin
> (3) sudo chmod +x dsspcmbi
> - do_dssp did not work.
>
> Then I (a) renamed dsspcmbi to dssp (b) ln -s dsspcmbi dssp
> - do_dssp still did not work.
>
> Then I did : export DSSP=/usr/local/bin/dssp
> - do_dssp still did not work as well.
>
>
> Please advise.
> Deb.
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-- 
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Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
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[gmx-users] do_dssp segmental fault

[Debajyoti Ghosh]

Dear gmx users,
I recently upgraded the operating system to Ubuntu 12 and re-installed
Gromacs 4.5.5. But I could not re-install dssp.

I did the following:
(1) I downloaded dsspcmbi from http://swift.cmbi.ru.nl/gv/dssp/
Went to distributions- DSSPold - Linux Distributions to download
dsspcmbi. (2) Moved to /usr/local/bin
(3) sudo chmod +x dsspcmbi
- do_dssp did not work.

Then I (a) renamed dsspcmbi to dssp (b) ln -s dsspcmbi dssp
- do_dssp still did not work.

Then I did : export DSSP=/usr/local/bin/dssp
- do_dssp still did not work as well.


Please advise.
Deb.
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Re: [gmx-users] do_dssp segmentation fault error

[Justin A. Lemkul]

On 5/16/12 5:57 AM, bunty xy wrote:

Hello Friends
I have installed GROMACS 4.5.5 on linux.
I put the DSSP Executable in /usr/local/bin
when i run the following command:
do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm


i got the following error.
Reading file md.tpr, VERSION 4.5.5 (single precision)
Reading file md.tpr, VERSION 4.5.5 (single precision)
Segmentation fault


Please tell me how can i resolve this " Segmentation fault"   error.


This same question was posed just a little bit earlier.  You need to make sure 
you're using the right version of DSSP (the old one).


-Justin

--


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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp segmentation fault error

[bunty xy]

Hello Friends
I have installed GROMACS 4.5.5 on linux.
I put the DSSP Executable in /usr/local/bin
when i run the following command:
do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm


i got the following error.
Reading file md.tpr, VERSION 4.5.5 (single precision)
Reading file md.tpr, VERSION 4.5.5 (single precision)
Segmentation fault


Please tell me how can i resolve this " Segmentation fault"   error.
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

Bernhard Knapp wrote:
The problem with this solution is that I would have to recompile gromacs 
on all maschines were I want to use dssp, right? Is there an older 
version of dssp still available from somewhere? On the dssp-homepage I 
found unfortunatly only the current but no past versions of dssp...




There are indeed old versions on the DSSP homepage (I was unaware of that until 
Mark's reply, which made me poke around).  Under Miscellaneous -> Distribution, 
there is a heading called "DSSPold" that appears to contain the old version of 
the program.


-Justin


best,
Bernhard



Am 04.04.2012 14:03, schrieb gmx-users-requ...@gromacs.org:

Bernhard Knapp wrote:

>  Hi
>  >  I have some problems to get do_dssp running:
>  >  I downloaded the binary of dssp 
fromhttp://swift.cmbi.ru.nl/gv/dssp/  .
>  Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I 
copied
>  it to the correct location: "cp dssp-2-linux-i386 
/usr/local/bin/dssp"

>  and gave the user the right to execute the binary.
>  If I call dssp in an arbitrary directory (e.g.  "dssp -i test.pdb -o
>  test.dssp") it works fine.  However, if I call it via do_dssp (e.g.
>  "do_dssp -f test.xtc -s test.tpr -o test.xpm") I get the following
>  error: "Fatal error: Failed to execute command: 
/usr/local/bin/dssp -na

>  ddZ2pWoM ddjmIN4j>  /dev/null 2>  /dev/null". If I try to see what is
>  going wrong via executing "/usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j"
>  directly in the shell then I get "unknown option -n".
>  >  Google did not help me since most people who got this error had 
dssp in
>  the wrong path. In my case it definitly finds the executable but 
in the

>  execution something goes wrong ...
>  >  What am I doing wrong?
>  
The problem is that the dssp syntax has changed and the Gromacs code 
currently
can't handle that syntax.  A patch has been proposed in the 
development version
but it has not yet been incorporated into the git repository.  You 
could make

the modifications to the source yourself by following:

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

-Justin


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[Mark Abraham]

On 4/04/2012 10:02 PM, Justin A. Lemkul wrote:



Bernhard Knapp wrote:

Hi

I have some problems to get do_dssp running:

I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ 
. Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I 
copied it to the correct location: "cp dssp-2-linux-i386 
/usr/local/bin/dssp" and gave the user the right to execute the binary.
If I call dssp in an arbitrary directory (e.g.  "dssp -i test.pdb -o 
test.dssp") it works fine.  However, if I call it via do_dssp (e.g. 
"do_dssp -f test.xtc -s test.tpr -o test.xpm") I get the following 
error: "Fatal error: Failed to execute command: /usr/local/bin/dssp 
-na ddZ2pWoM ddjmIN4j > /dev/null 2> /dev/null". If I try to see what 
is going wrong via executing "/usr/local/bin/dssp -na ddZ2pWoM 
ddjmIN4j" directly in the shell then I get "unknown option -n".


Google did not help me since most people who got this error had dssp 
in the wrong path. In my case it definitly finds the executable but 
in the execution something goes wrong ...


What am I doing wrong?



The problem is that the dssp syntax has changed and the Gromacs code 
currently can't handle that syntax.  A patch has been proposed in the 
development version but it has not yet been incorporated into the git 
repository.  You could make the modifications to the source yourself 
by following:


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


Or dig around on the dssp site to get the old version.

Mark
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

Bernhard Knapp wrote:

Hi

I have some problems to get do_dssp running:

I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . 
Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I copied 
it to the correct location: "cp dssp-2-linux-i386 /usr/local/bin/dssp" 
and gave the user the right to execute the binary.
If I call dssp in an arbitrary directory (e.g.  "dssp -i test.pdb -o 
test.dssp") it works fine.  However, if I call it via do_dssp (e.g. 
"do_dssp -f test.xtc -s test.tpr -o test.xpm") I get the following 
error: "Fatal error: Failed to execute command: /usr/local/bin/dssp -na 
ddZ2pWoM ddjmIN4j > /dev/null 2> /dev/null". If I try to see what is 
going wrong via executing "/usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j" 
directly in the shell then I get "unknown option -n".


Google did not help me since most people who got this error had dssp in 
the wrong path. In my case it definitly finds the executable but in the 
execution something goes wrong ...


What am I doing wrong?



The problem is that the dssp syntax has changed and the Gromacs code currently 
can't handle that syntax.  A patch has been proposed in the development version 
but it has not yet been incorporated into the git repository.  You could make 
the modifications to the source yourself by following:


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

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp

[Bernhard Knapp]

Hi

I have some problems to get do_dssp running:

I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using 
"gunzip dssp-2-linux-i386.gz". Next I copied it to the correct location: "cp 
dssp-2-linux-i386 /usr/local/bin/dssp" and gave the user the right to execute the binary.
If I call dssp in an arbitrary directory (e.g.  "dssp -i test.pdb -o test.dssp") it works fine.  However, if I call it via 
do_dssp (e.g. "do_dssp -f test.xtc -s test.tpr -o test.xpm") I get the following error: "Fatal error: Failed to execute 
command: /usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j > /dev/null 2> /dev/null". If I try to see what is going wrong via 
executing "/usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j" directly in the shell then I get "unknown option -n".

Google did not help me since most people who got this error had dssp in the 
wrong path. In my case it definitly finds the executable but in the execution 
something goes wrong ...

What am I doing wrong?

best,
Bernhard



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Re: [gmx-users] do_dssp segmentation fault

[Mark Abraham]

On 3/03/2012 6:21 PM, arun kumar wrote:
yes other gromacs tools are working properly ...i installed gromacs in 
/usr/local/
so i used the command /usr/local/gromacs/bin/./do_dssp -s md.tpr -f 
md.xtc -o ss.xpm
and i also set the environment variable as export 
DSSP=/usr/local/gromacs/bin/do_dssp


You should have posted all of this information last time. See do_dssp -h 
for how to set DSSP in a way that will actually have a chance of 
working. And if it still doesn't work, do the other half of the tests I 
suggested last time before posting again :-)


Mark
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Re: [gmx-users] do_dssp segmentation fault

[Mark Abraham]

On 3/03/2012 5:14 PM, arun kumar wrote:

Dear all,

Iam trying to generate secondary structure plot through do_dssp 
program, but there was an error like "segmentation fault"


Reading file md.tpr, VERSION 4.0.7 (single precision)
Reading file md.tpr, VERSION 4.0.7 (single precision)
Segmentation fault (core dumped)
bash-4.1#

can anybody please say what it means and how to solve it


No, because there's no diagnostic information. Do other GROMACS tools 
work? Does the DSSP executable work?


Mark
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[gmx-users] do_dssp segmentation fault

[arun kumar]

Dear all,

Iam trying to generate secondary structure plot through do_dssp program,
but there was an error like "segmentation fault"

Reading file md.tpr, VERSION 4.0.7 (single precision)
Reading file md.tpr, VERSION 4.0.7 (single precision)
Segmentation fault (core dumped)
bash-4.1#

can anybody please say what it means and how to solve it

Regards,
-- 
Arun Kumar Somavarapu
Project-JRF
Dr. Prasanna's lab
TMC, ACTREC
Navi Mumbai-410210
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Re: [gmx-users] do_dssp segmentation fault

[Carsten Kutzner]

Hi,

On Nov 23, 2011, at 8:24 AM, Alex Jemulin wrote:

> Thanks for your reply
> Could you tell me the name of the file to download and how to install it?
Please follow the instructions at 
http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage and
http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial.

In short:
git clone git://git.gromacs.org/gromacs.git
git checkout --track -b release-4-5-patches origin/release-4-5-patches

If you are using CMake, you can then just install this like the normal
.tar.gz distributions from the gromacs home page. If you are using autotools,
do a ./bootstrap before the configure step.

Best,
  Carsten


>  
> Bests
> 
> Da: Carsten Kutzner 
> A: Alex Jemulin ; Discussion list for GROMACS users 
>  
> Inviato: Martedì 22 Novembre 2011 13:25
> Oggetto: Re: [gmx-users] do_dssp segmentation fault
> 
> Dear Alex,
> 
> On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote:
> 
> > Dear all
> > I'm experiencing the following error in Gromacs 4.5 with do_dssp
> >  
> > Here is the command
> > do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc 
> > secondary-structure.xvg -dt 10
> >  
> > give me the following error
> > segmentation fault
> >  
> > How can I fix it?
> I removed a segmentation fault in do_dssp a couple of weeks ago but this is
> post version 4.5.5. So you need to check out the current release-4-5-patches 
> from
> the git server. I believe this will fix your problem.
> 
> Carsten
> 
> >  
> > Thank in ad
> > -- 
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> 
> 
> 

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Re: [gmx-users] do_dssp segmentation fault

[Carsten Kutzner]

Dear Alex,

On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote:

> Dear all
> I'm experiencing the following error in Gromacs 4.5 with do_dssp
>  
> Here is the command
> do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc 
> secondary-structure.xvg -dt 10
>  
> give me the following error
> segmentation fault
>  
> How can I fix it?
I removed a segmentation fault in do_dssp a couple of weeks ago but this is
post version 4.5.5. So you need to check out the current release-4-5-patches 
from
the git server. I believe this will fix your problem.

Carsten
 
>  
> Thank in ad
> -- 
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Re: [gmx-users] do_dssp segmentation fault

[Mark Abraham]

On 22/11/2011 7:28 PM, Alex Jemulin wrote:

Dear all
I'm experiencing the following error in Gromacs 4.5 with do_dssp
Here is the command
do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc 
secondary-structure.xvg -dt 10

give me the following error
segmentation fault
How can I fix it?



Make sure you have followed all the instructions available with do_dssp 
-h, and that your DSSP is the old version, not the updated one.


Mark
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[gmx-users] do_dssp segmentation fault

[Alex Jemulin]

Dear all
I'm experiencing the following error in Gromacs 4.5 with do_dssp

Here is the command
do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc 
secondary-structure.xvg -dt 10

give me the following error
segmentation fault

How can I fix it?

Thank in ad-- 
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[gmx-users] do_dssp normalization error

[loan . huynh]

Dear Gromacs users,

I used do_dssp to calculate the secondary structure of peptide. From  
the output scount.xvg file, the last column shows the number of  
residues that is "chain separator". At the end of the scount.xvg file,  
the last line provide the percentage of different secondary  
structures. The unusual is the normalization includes the "chain  
separator" column (see a example below). This seems like an error. Is  
there any other suggestion? I re-calculate the percentage of various  
secondary structures and leave the "chain separator" out.


Thank you,
Loan

For example:

# do_dssp is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@title "Secondary Structure"
@xaxis  label "Time (ps)"
@yaxis  label "Number of Residues"
@TYPE xy
@ subtitle "Structure =  +  +  + Turn"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "Bend"
@ s3 legend "Turn"
@ s4 legend "Chain_Separator"
   81232 412 7
  121033 510 7
  161032 610 7
  201032 610 7
# Totals42   129214228
# SS %0.19  0.59  0.10  0.19  0.13





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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

afsaneh maleki wrote:

Hi,

I'm trying to use do_dssp of gromacs 4.5.4 in fedora core .

I did processes of Download , Uncompress and Compile the source code as 
the following


unzip dsspcmbi.zip

cd dssp
 
[root@localhost dssp]# ./DsspCompileGCC

That i got this message:

Running script to compile the CMBI version of DSSP, please wait...
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status
Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program...

I googled but i don't find clear way to solve this problem.
can help me?



Really?  All the Google results seem to point to the same solution involving 
installing glibc-devel or some such suitably named package for whatever your 
system is.


Otherwise, contact the DSSP developers so they can tell you the prerequisites.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp

[afsaneh maleki]

Hi,

I'm trying to use do_dssp of gromacs 4.5.4 in fedora core .

I did processes of Download , Uncompress and Compile the source code as the
following

unzip dsspcmbi.zip

cd dssp

[root@localhost dssp]# ./DsspCompileGCC
That i got this message:

Running script to compile the CMBI version of DSSP, please wait...
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status
Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program...

I googled but i don't find clear way to solve this problem.
can help me?


Afsaneh
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[gmx-users] DO_DSSP

[anna]

Thank you very much!

Anna


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Re: [gmx-users] DO_DSSP

[Mark Abraham]

On 6/05/2011 5:22 PM, battis...@libero.it wrote:


Dear all,


I'm trying install do_dssp on my pc.

I followed the steps indicated in the page:

http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html


>> 1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf 
dsspcmbi.tar.gz

>> 2.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp#./DsspCompileGCC
>> 3.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# cp dsspcmbi dssp
>> 4.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# mv dssp 
/usr/local/bin



and the program work well.


Now my question:

How the program use the file that I downloaded from the web-page:

http://swift.cmbi.ru.nl/gv/dssp/   using the indicated instruction?



GROMACS doesn't. Read the DSSP documentation about what it is providing.

(I found this page from 
http://www.gromacs.org/Developer_Zone/Programming_Guide/DSSP)


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

The link  rsync://rsync.cmbi.ru.nl/dssp/  is one of the best 
//database //to calculate the angle into the secondary structures and 
so to define that, isn't it?




One doesn't need a database to calculate angles.

Mark
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[gmx-users] DO_DSSP

[battis...@libero.it]

Dear all,

I'm trying install do_dssp on my pc.I followed the steps indicated in the page:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html
>> 1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf dsspcmbi.tar.gz
>> 2.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp#./DsspCompileGCC
>> 3.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# cp dsspcmbi dssp
>> 4.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# mv dssp /usr/local/bin
and the program work well.
Now my question:How the program use the file that I downloaded from the 
web-page:http://swift.cmbi.ru.nl/gv/dssp/   using the indicated instruction? (I 
found this page from 
http://www.gromacs.org/Developer_Zone/Programming_Guide/DSSP)

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

The link  rsync://rsync.cmbi.ru.nl/dssp/  is one of the best  database to 
calculate the angle into the secondary structures and so to define that, isn't 
it?

Thanks,
Anna
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Re: [gmx-users] do_dssp failed to execute

[Justin A. Lemkul]

Sunita Patel wrote:

***
*Dear Mark,

On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote
 > - Original Message -
 > From: Sunita Patel 
 > Date: Monday, October 11, 2010 22:50
 > Subject: [gmx-users] do_dssp  failed to execute
 > To: Discussion list for GROMACS users 
 >
 > > Dear User,
 > >
 > > I set the path for dssp executable in .bashrc file. Still
 >
 > dssp in the path is probably not sufficient. See 
http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

 >
I already seen this page and the dssp executable file is present in the 
specified location.
I surprise why it was not working before. I freshly downloaded the 
dsspcmbi executable and rename it to dssp and gave executable file 
permission and it started working.


I was doing like this earlier also. May be dssp executable was corrupted.


I would suspect something else was going on.  Note from the error message that 
the dssp executable was not even invoked:


Failed to execute command: /home/sunita/soft/bin -na ...

Thus, do_dssp was trying to execute "bin" instead of "dssp."

The DSSP environment variable must point to the dssp executable itself, not the 
PATH to it.  Maybe you've got things working now, but do check to make sure 
you've got your environment properly configured to save yourself headaches later.


-Justin


Thanks,
Sunita

 > Mark
 >
 > > getting following
 > > error. Could anybody suggest what would be the problem.
 > >
 > > error message
 > > Select a group: 5
 > > Selected 5: 'MainChain'
 > > There are 134 residues in your selected group
 > > Opening library file
 > > /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading
 > > frame0
 > > time0.000   
 > > Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1#

 > >
 > > ---
 > > Program do_dssp, VERSION 4.0.7
 > > Source code file: do_dssp.c, line: 471
 > >
 > > Fatal error:
 > > Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3
 > > ddZl9dcf >
 > > /dev/null 2> /dev/null
 > > **
 > >
 > > Thanks,
 > > Sunit
 > >
 > >
 > > -
 > > --
 > > gmx-users mailing listgmx-users@gromacs.org
 > > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > Please search the archive at
 > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > > Please don't post (un)subscribe requests to the list. Use the
 > > www interface or send it to gmx-users-requ...@gromacs.org.
 > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


Dr. Sunita Patel
-
Visiting Fellow
Department of Chemical Sciences
T.I.F.R., Homi Bhabha Road, Colaba
Mumbai - 45
-



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp failed to execute

[Sunita Patel]

Dear Mark,

On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote
> - Original Message -
> From: Sunita Patel 
> Date: Monday, October 11, 2010 22:50
> Subject: [gmx-users] do_dssp  failed to execute
> To: Discussion list for GROMACS users 
> 
> > Dear User,
> > 
> > I set the path for dssp executable in .bashrc file. Still 
> 
> dssp in the path is probably not sufficient. See 
> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
> 
I already seen this page and the dssp executable file is present in the 
specified location. 
I surprise why it was not working before. I freshly downloaded the dsspcmbi 
executable and rename it to dssp and gave executable file permission and it 
started working.

I was doing like this earlier also. May be dssp executable was corrupted. 
Thanks,
Sunita

> Mark
> 
> > getting following
> > error. Could anybody suggest what would be the problem. 
> > 
> > error message
> > Select a group: 5
> > Selected 5: 'MainChain'
> > There are 134 residues in your selected group
> > Opening library file 
> > /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading 
> > frame   0 
> > time    0.000   
> > Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1#
> > 
> > ---
> > Program do_dssp, VERSION 4.0.7
> > Source code file: do_dssp.c, line: 471
> > 
> > Fatal error:
> > Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 
> > ddZl9dcf >
> > /dev/null 2> /dev/null
> > **
> > 
> > Thanks,
> > Sunit
> > 
> > 
> > -
> > -- 
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Dr. Sunita Patel 
- 
Visiting Fellow 
Department of Chemical Sciences 
T.I.F.R., Homi Bhabha Road, Colaba 
Mumbai - 45 
-
 
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Re: [gmx-users] do_dssp failed to execute

[Mark Abraham]

- Original Message -
From: Sunita Patel 
Date: Monday, October 11, 2010 22:50
Subject: [gmx-users] do_dssp  failed to execute
To: Discussion list for GROMACS users 

> Dear User,
> 
> I set the path for dssp executable in .bashrc file. Still 

dssp in the path is probably not sufficient. See 
http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

Mark

> getting following
> error. Could anybody suggest what would be the problem. 
> 
> error message
> Select a group: 5
> Selected 5: 'MainChain'
> There are 134 residues in your selected group
> Opening library file 
> /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading 
> frame   0 
> time0.000   
> Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1#
> 
> ---
> Program do_dssp, VERSION 4.0.7
> Source code file: do_dssp.c, line: 471
> 
> Fatal error:
> Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 
> ddZl9dcf >
> /dev/null 2> /dev/null
> **
> 
> Thanks,
> Sunit
> 
> 
> -
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] do_dssp failed to execute

[Sunita Patel]

Dear User,

I set the path for dssp executable in .bashrc file. Still getting following
error. Could anybody suggest what would be the problem. 

error message
Select a group: 5
Selected 5: 'MainChain'
There are 134 residues in your selected group
Opening library file /home/sunita/soft/gromacs/share/gromacs/top/ss.map
Reading frame   0 time0.000   
Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1#

---
Program do_dssp, VERSION 4.0.7
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 ddZl9dcf >
/dev/null 2> /dev/null
**

Thanks,
Sunit


-
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Re: [gmx-users] do_dssp fatal error

[Paymon Pirzadeh]

Dear Justin,
Thanks a lot. Your comment was very instructive. So, I use Mainchain
(group 5) for future.

Paymon


On Wed, 2010-10-06 at 12:41 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Hello,
> > To investigate the secondary structure I issued the do_dssp command as
> > follows:
> > 
> >  do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
> > AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
> > AFPIII_Ih0001_81_93_NpT265
> > 
> > Then, I had read somewhere in the archive to select the alpha carbons
> > for accurate results, and I did, but the following error pops up:
> > 
> 
> Then you read an inaccurate post.  At the very least, all MainChain atoms 
> must 
> be considered.  Think about how the DSSP algorithm works - assessment of 
> hydrogen bonding patterns.  Can these patterns be determined by using only 
> alpha 
> carbons?
> 
> I know I have posted several times about how to properly use do_dssp, and it 
> is 
> also on the wiki:
> 
> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
> 
> > Program do_dssp_d_mpi, VERSION 4.0.5
> > Source code file: do_dssp.c, line: 471
> > 
> > Fatal error:
> > Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
> > ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null
> > 
> > The cluster technician tested the forwarded procedure (appended below),
> > and it seems that the backbone structure has some problems. I will be
> > appreciated if one tells me is it really a problem with backbone or sth
> > with installation of dssp. If problem is with backbone, then why pdb2gmx
> > did not issue any warnings?
> 
> The results below indicate that the command works correctly for groups that 
> contain all the necessary atoms.  Failures only occur when other, incorrect, 
> groups are used.
> 
> -Justin
> 
> > Regards,
> > 
> > Paymon
> > 
> > 
> > 
> > 
> > Subject:
> > RE: Sorry + Re: GROMACS utilities
> > From:
> > Roman Baranowski 
> > Date:
> > Tue, 5 Oct 2010 19:31:23 -0700 (PDT)
> > To:
> > Paymon Pirzadeh 
> > 
> > To:
> > Paymon Pirzadeh 
> > 
> > 
> > 
> > Dear Paymon,
> > 
> > I have interrupted the run (it was taking too long) and I did not want 
> > to prevent you from work in that directory. For:
> > Opening library file 
> > /global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat
> > Group 0 (  System) has 293280 elements
> > Group 1 ( Protein) has  1002 elements
> > Group 2 (   Protein-H) has   485 elements
> > Group 3 ( C-alpha) has66 elements
> > Group 4 (Backbone) has   198 elements
> > Group 5 (   MainChain) has   265 elements
> > Group 6 (MainChain+Cb) has   328 elements
> > Group 7 ( MainChain+H) has   327 elements
> > Group 8 (   SideChain) has   675 elements
> > Group 9 ( SideChain-H) has   220 elements
> > Group10 ( Prot-Masses) has  1002 elements
> > Group11 ( Non-Protein) has 292278 elements
> > Group12 ( SOL) has 292278 elements
> > Group13 (   Other) has 292278 elements
> > 
> > 0,1,2,5,6,7 work but
> > 3,4,8,9,10,11,12 and 13 do not. However the output
> > Fatal error:
> > Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na 
> > ddNPsTyg dda8k3CK
> > suggests that there is some problem with the input. So tried to run
> > dssp -na ddNPsTyg dda8k3CK
> > interactively (without do_dssp_d_mpi -f AFPIII ...) and:
> > 
> > dssp -na ddNPsTyg dda8k3CK
> > (I have used the full path i.e.:
> > /global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP)
> > 
> > the output is (I remove most of the lines as they do not seem to be 
> > relevant):
> >  !!! Backbone incomplete for residue ALA1
> >  residue will be ignored !!!
> > 
> >  !!! Backbone incomplete for residue ASN2
> >  residue will be ignored !!!
> > 
> >  !!! Backbone incomplete for residue GLN3
> >  residue will be ignored !!!
> > ...
> > ..
> > 
> >  !!! Backbone incomplete for residue ALA   66
> >  residue will be ignored !!!
> > 
> >  !!! HEADER-card missing !!!
> >  !!! COMPOUND-card missing !!!
> >  !!! SOURCE-card missing !!!
> >  !!! AUTHOR-card missing !!!
> >  !!! No residue with complete backbone !!!
> > 
> > So it once again suggests the input issue. I do not know too much about 
> > Gromacs and dssp setup but it clearly points to input.
> > 
> > All the best
> > Roman
> > 
> > 
> > 
> > On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:
> > 
> >> Dear Roman,
> >> do_dssp does analysis on secondary structure of proteins. It is written
> >> on online blogs that to get the correct results, you should select alpha
> >> carbons, option 3. However, the only problem that might be the case is
> >> providing an index file of backbone alpha carbones which looks
> >> irrelevant since do_dssp asks about the group interactively. I don't
> >> know if I can try the comm

Re: [gmx-users] do_dssp fatal error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:

 do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Then, I had read somewhere in the archive to select the alpha carbons
for accurate results, and I did, but the following error pops up:



Then you read an inaccurate post.  At the very least, all MainChain atoms must 
be considered.  Think about how the DSSP algorithm works - assessment of 
hydrogen bonding patterns.  Can these patterns be determined by using only alpha 
carbons?


I know I have posted several times about how to properly use do_dssp, and it is 
also on the wiki:


http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp


Program do_dssp_d_mpi, VERSION 4.0.5
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null

The cluster technician tested the forwarded procedure (appended below),
and it seems that the backbone structure has some problems. I will be
appreciated if one tells me is it really a problem with backbone or sth
with installation of dssp. If problem is with backbone, then why pdb2gmx
did not issue any warnings?


The results below indicate that the command works correctly for groups that 
contain all the necessary atoms.  Failures only occur when other, incorrect, 
groups are used.


-Justin


Regards,

Paymon




Subject:
RE: Sorry + Re: GROMACS utilities
From:
Roman Baranowski 
Date:
Tue, 5 Oct 2010 19:31:23 -0700 (PDT)
To:
Paymon Pirzadeh 

To:
Paymon Pirzadeh 



Dear Paymon,

I have interrupted the run (it was taking too long) and I did not want 
to prevent you from work in that directory. For:
Opening library file 
/global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat

Group 0 (  System) has 293280 elements
Group 1 ( Protein) has  1002 elements
Group 2 (   Protein-H) has   485 elements
Group 3 ( C-alpha) has66 elements
Group 4 (Backbone) has   198 elements
Group 5 (   MainChain) has   265 elements
Group 6 (MainChain+Cb) has   328 elements
Group 7 ( MainChain+H) has   327 elements
Group 8 (   SideChain) has   675 elements
Group 9 ( SideChain-H) has   220 elements
Group10 ( Prot-Masses) has  1002 elements
Group11 ( Non-Protein) has 292278 elements
Group12 ( SOL) has 292278 elements
Group13 (   Other) has 292278 elements

0,1,2,5,6,7 work but
3,4,8,9,10,11,12 and 13 do not. However the output
Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na 
ddNPsTyg dda8k3CK

suggests that there is some problem with the input. So tried to run
dssp -na ddNPsTyg dda8k3CK
interactively (without do_dssp_d_mpi -f AFPIII ...) and:

dssp -na ddNPsTyg dda8k3CK
(I have used the full path i.e.:
/global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP)

the output is (I remove most of the lines as they do not seem to be 
relevant):

 !!! Backbone incomplete for residue ALA1
 residue will be ignored !!!

 !!! Backbone incomplete for residue ASN2
 residue will be ignored !!!

 !!! Backbone incomplete for residue GLN3
 residue will be ignored !!!
...
..

 !!! Backbone incomplete for residue ALA   66
 residue will be ignored !!!

 !!! HEADER-card missing !!!
 !!! COMPOUND-card missing !!!
 !!! SOURCE-card missing !!!
 !!! AUTHOR-card missing !!!
 !!! No residue with complete backbone !!!

So it once again suggests the input issue. I do not know too much about 
Gromacs and dssp setup but it clearly points to input.


All the best
Roman



On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:


Dear Roman,
do_dssp does analysis on secondary structure of proteins. It is written
on online blogs that to get the correct results, you should select alpha
carbons, option 3. However, the only problem that might be the case is
providing an index file of backbone alpha carbones which looks
irrelevant since do_dssp asks about the group interactively. I don't
know if I can try the command or not (since you mentioned it is
running), but you may try it again with group option 3.
Regards,

Paymon


On Tue, 2010-10-05 at 16:40 -0700, Roman Baranowski wrote:


 Dear Paymon,

I have just log in as you, cd to:
GROMACS/proteins/AFP-III/Ih0001/81_93_204/AFPIII_Ih0001_81_93_NpT265_round1 


  and issued
module load gromacs
and than:
do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Select a group: 0
Selected 0: 'System'
There are 48779 residues in your selected group
Opening library file
/global/software/gromacs/4.0.5/intel/share/gromacs/top/ss.map
Reading frame

[gmx-users] do_dssp fatal error

[Paymon Pirzadeh]

Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:

 do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Then, I had read somewhere in the archive to select the alpha carbons
for accurate results, and I did, but the following error pops up:

Program do_dssp_d_mpi, VERSION 4.0.5
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null

The cluster technician tested the forwarded procedure (appended below),
and it seems that the backbone structure has some problems. I will be
appreciated if one tells me is it really a problem with backbone or sth
with installation of dssp. If problem is with backbone, then why pdb2gmx
did not issue any warnings?
Regards,

Paymon
--- Begin Message ---


Dear Paymon,

I have interrupted the run (it was taking too long) and I did not want to 
prevent you from work in that directory. For:
Opening library file 
/global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat

Group 0 (  System) has 293280 elements
Group 1 ( Protein) has  1002 elements
Group 2 (   Protein-H) has   485 elements
Group 3 ( C-alpha) has66 elements
Group 4 (Backbone) has   198 elements
Group 5 (   MainChain) has   265 elements
Group 6 (MainChain+Cb) has   328 elements
Group 7 ( MainChain+H) has   327 elements
Group 8 (   SideChain) has   675 elements
Group 9 ( SideChain-H) has   220 elements
Group10 ( Prot-Masses) has  1002 elements
Group11 ( Non-Protein) has 292278 elements
Group12 ( SOL) has 292278 elements
Group13 (   Other) has 292278 elements

0,1,2,5,6,7 work but
3,4,8,9,10,11,12 and 13 do not. However the output
Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na 
ddNPsTyg dda8k3CK

suggests that there is some problem with the input. So tried to run
dssp -na ddNPsTyg dda8k3CK
interactively (without do_dssp_d_mpi -f AFPIII ...) and:

dssp -na ddNPsTyg dda8k3CK
(I have used the full path i.e.:
/global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP)

the output is (I remove most of the lines as they do not seem to be 
relevant):

 !!! Backbone incomplete for residue ALA1
 residue will be ignored !!!

 !!! Backbone incomplete for residue ASN2
 residue will be ignored !!!

 !!! Backbone incomplete for residue GLN3
 residue will be ignored !!!
...
..

 !!! Backbone incomplete for residue ALA   66
 residue will be ignored !!!

 !!! HEADER-card missing !!!
 !!! COMPOUND-card missing !!!
 !!! SOURCE-card missing !!!
 !!! AUTHOR-card missing !!!
 !!! No residue with complete backbone !!!

So it once again suggests the input issue. I do not know too much about 
Gromacs and dssp setup but it clearly points to input.


All the best
Roman



On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:


Dear Roman,
do_dssp does analysis on secondary structure of proteins. It is written
on online blogs that to get the correct results, you should select alpha
carbons, option 3. However, the only problem that might be the case is
providing an index file of backbone alpha carbones which looks
irrelevant since do_dssp asks about the group interactively. I don't
know if I can try the command or not (since you mentioned it is
running), but you may try it again with group option 3.
Regards,

Paymon


On Tue, 2010-10-05 at 16:40 -0700, Roman Baranowski wrote:


Dear Paymon,

I have just log in as you, cd to:
GROMACS/proteins/AFP-III/Ih0001/81_93_204/AFPIII_Ih0001_81_93_NpT265_round1
  and issued
module load gromacs
and than:
do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Select a group: 0
Selected 0: 'System'
There are 48779 residues in your selected group
Opening library file
/global/software/gromacs/4.0.5/intel/share/gromacs/top/ss.map
Reading frame   0 time0.000
Back Off! I just backed up ddOjBDfr to ./#ddOjBDfr.1#
Reading frame   1 time   10.000
Reading frame  50 time  500.000

and it is still running , is it possible  that there is a need for some
extra maps or databases used by dssp in the share directory.

All the best
Roman


On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:


Dear Roman,
I tried it again and the still same error:

Program do_dssp_d_mpi, VERSION 4.0.5
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
dd4qT1kw ddhRhEOb > /dev/null 2> /dev/null

The command I used was

do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

The location of 

Re: [gmx-users] do_dssp

[Justin A. Lemkul]

shahid nayeem wrote:

Hi
No i dont have any capping group


Then I have no idea what's going on.  The only data that present a problem are 
in the very first frame, indicating that the HEBT+coil content totals 80 
residues.  All the other frames look fine.  It could be that the algorithm is 
detecting different structural features for the same residue (i.e., they are 
somewhat ambiguous), but I have never heard of such an issue.


-Justin


shahid Nayeem

 
On 5/24/10, *Justin A. Lemkul* > wrote:




shahid nayeem wrote:

Hi Justin
I choose group 5 main chain for dssp calculation


Do you have any capping groups (N-acetyl, C-amine, etc)?

-Justin

Shahid Nayeem


 On 5/24/10, *Justin A. Lemkul* mailto:jalem...@vt.edu> >> wrote:



   shahid nayeem wrote:

   Dear All
   I did 10ns simulation of three peptide residue solvated in
   water. Each peptide residue is 26 residue long. In final .gro
   file it is showing total 78 residue which is O.K. as 3x26=78.
   For inserting three similar peptide I used genconf
command. when
   I run dssp I get total residue as 80. The command for dssp is
   do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part
of the
   output of dssp run is as follows.


   When prompted, what group did you choose for the analysis?

   -Justin


   @ s0 legend "Structure"

 
   @ s1 legend "Coil"


 
   @ s2 legend "B-Sheet"


 
   @ s3 legend "B-Bridge"


 
   @ s4 legend "Bend"


 
   @ s5 legend "Turn"


 
   @ s6 legend "A-Helix"


 
   @ s7 legend "5-Helix"


 
   @ s8 legend "3-Helix"


 
 04624 0 0 71036 0 3


103926 0 015 435 0 0

203729 0 011 433 0 3

303732 0 011 235 0 0

403631 0 010 630 0 3

504130 0 0 91031 0 0

   Please suggest why I am not getting the actual number of
residue
   in dssp file.
   When I follow the same procedure for full protein molecule
   simulation I get the same number of residue in dssp output as
   well as final.gro file
   shahid nayeem


   -- 

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080
   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   
   -- gmx-users mailing listgmx-users@gromacs.org

   >
   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search before
   posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.
   Can't post? Read http://www.gromacs.org/mailing_lists/users.php



-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
gmx-users mailing listgmx-users@gromacs.org


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Please search the archive at http://www.gromacs.org/search before
posting!
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--
=

Re: [gmx-users] do_dssp

[shahid nayeem]

Hi
No i dont have any capping group
shahid Nayeem


On 5/24/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> Hi Justin
>> I choose group 5 main chain for dssp calculation
>>
>
> Do you have any capping groups (N-acetyl, C-amine, etc)?
>
> -Justin
>
> Shahid Nayeem
>>
>>
>>  On 5/24/10, *Justin A. Lemkul* mailto:jalem...@vt.edu>>
>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear All
>>I did 10ns simulation of three peptide residue solvated in
>>water. Each peptide residue is 26 residue long. In final .gro
>>file it is showing total 78 residue which is O.K. as 3x26=78.
>>For inserting three similar peptide I used genconf command. when
>>I run dssp I get total residue as 80. The command for dssp is
>>do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
>>output of dssp run is as follows.
>>
>>
>>When prompted, what group did you choose for the analysis?
>>
>>-Justin
>>
>>
>>@ s0 legend "Structure"
>>
>>
>>@ s1 legend "Coil"
>>
>>
>>@ s2 legend "B-Sheet"
>>
>>
>>@ s3 legend "B-Bridge"
>>
>>
>>@ s4 legend "Bend"
>>
>>
>>@ s5 legend "Turn"
>>
>>
>>@ s6 legend "A-Helix"
>>
>>
>>@ s7 legend "5-Helix"
>>
>>
>>@ s8 legend "3-Helix"
>>
>>
>>  04624 0 0 71036 0 3
>>
>> 103926 0 015 435 0 0
>>
>> 203729 0 011 433 0 3
>>
>> 303732 0 011 235 0 0
>>
>> 403631 0 010 630 0 3
>>
>> 504130 0 0 91031 0 0
>>
>>Please suggest why I am not getting the actual number of residue
>>in dssp file.
>>When I follow the same procedure for full protein molecule
>>simulation I get the same number of residue in dssp output as
>>well as final.gro file
>>shahid nayeem
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

shahid nayeem wrote:

Hi Justin
I choose group 5 main chain for dssp calculation


Do you have any capping groups (N-acetyl, C-amine, etc)?

-Justin


Shahid Nayeem

 
On 5/24/10, *Justin A. Lemkul* > wrote:




shahid nayeem wrote:

Dear All
I did 10ns simulation of three peptide residue solvated in
water. Each peptide residue is 26 residue long. In final .gro
file it is showing total 78 residue which is O.K. as 3x26=78.
For inserting three similar peptide I used genconf command. when
I run dssp I get total residue as 80. The command for dssp is
do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
output of dssp run is as follows.


When prompted, what group did you choose for the analysis?

-Justin


@ s0 legend "Structure"

   


@ s1 legend "Coil"

   


@ s2 legend "B-Sheet"

   


@ s3 legend "B-Bridge"

   


@ s4 legend "Bend"

   


@ s5 legend "Turn"

   


@ s6 legend "A-Helix"

   


@ s7 legend "5-Helix"

   


@ s8 legend "3-Helix"

   


  04624 0 0 71036 0 3

 103926 0 015 435 0 0

 203729 0 011 433 0 3

 303732 0 011 235 0 0

 403631 0 010 630 0 3

 504130 0 0 91031 0 0

Please suggest why I am not getting the actual number of residue
in dssp file.
When I follow the same procedure for full protein molecule
simulation I get the same number of residue in dssp output as
well as final.gro file
shahid nayeem


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
gmx-users mailing listgmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[shahid nayeem]

Hi Justin
I choose group 5 main chain for dssp calculation
Shahid Nayeem


On 5/24/10, Justin A. Lemkul  wrote:
>
>
>
> shahid nayeem wrote:
>
>> Dear All
>> I did 10ns simulation of three peptide residue solvated in water. Each
>> peptide residue is 26 residue long. In final .gro file it is showing total
>> 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I
>> used genconf command. when I run dssp I get total residue as 80. The command
>> for dssp is do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
>> output of dssp run is as follows.
>>
>
> When prompted, what group did you choose for the analysis?
>
> -Justin
>
>
>> @ s0 legend "Structure"
>>
>>
>>
>> @ s1 legend "Coil"
>>
>>
>>
>> @ s2 legend "B-Sheet"
>>
>>
>>
>> @ s3 legend "B-Bridge"
>>
>>
>>
>> @ s4 legend "Bend"
>>
>>
>>
>> @ s5 legend "Turn"
>>
>>
>>
>> @ s6 legend "A-Helix"
>>
>>
>>
>> @ s7 legend "5-Helix"
>>
>>
>>
>> @ s8 legend "3-Helix"
>>
>>
>>
>>   04624 0 0 71036 0 3
>>
>>  103926 0 015 435 0 0
>>
>>  203729 0 011 433 0 3
>>
>>  303732 0 011 235 0 0
>>
>>  403631 0 010 630 0 3
>>
>>  504130 0 0 91031 0 0
>>
>> Please suggest why I am not getting the actual number of residue in dssp
>> file.
>> When I follow the same procedure for full protein molecule simulation I
>> get the same number of residue in dssp output as well as final.gro file
>> shahid nayeem
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

shahid nayeem wrote:

Dear All
I did 10ns simulation of three peptide residue solvated in water. Each 
peptide residue is 26 residue long. In final .gro file it is showing 
total 78 residue which is O.K. as 3x26=78. For inserting three similar 
peptide I used genconf command. when I run dssp I get total residue as 
80. The command for dssp is do_dssp -f  .xtc -s .tpr -o ss.xpm -sc 
scount.xvg. Part of the output of dssp run is as follows.


When prompted, what group did you choose for the analysis?

-Justin



@ s0 legend "Structure"



@ s1 legend "Coil"



@ s2 legend "B-Sheet"



@ s3 legend "B-Bridge"



@ s4 legend "Bend"



@ s5 legend "Turn"



@ s6 legend "A-Helix"



@ s7 legend "5-Helix"



@ s8 legend "3-Helix"



   04624 0 0 71036 0 3

  103926 0 015 435 0 0

  203729 0 011 433 0 3

  303732 0 011 235 0 0

  403631 0 010 630 0 3

  504130 0 0 91031 0 0

Please suggest why I am not getting the actual number of residue in dssp 
file.
When I follow the same procedure for full protein molecule simulation I 
get the same number of residue in dssp output as well as final.gro file
shahid nayeem 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp

[shahid nayeem]

Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is showing total
78 residue which is O.K. as 3x26=78. For inserting three similar peptide I
used genconf command. when I run dssp I get total residue as 80. The command
for dssp is do_dssp -f  .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
output of dssp run is as follows.

@ s0 legend "Structure"

@ s1 legend "Coil"

@ s2 legend "B-Sheet"

@ s3 legend "B-Bridge"

@ s4 legend "Bend"

@ s5 legend "Turn"

@ s6 legend "A-Helix"

@ s7 legend "5-Helix"

@ s8 legend "3-Helix"

   04624 0 0 71036 0 3

  103926 0 015 435 0 0

  203729 0 011 433 0 3

  303732 0 011 235 0 0

  403631 0 010 630 0 3

  504130 0 0 91031 0 0
Please suggest why I am not getting the actual number of residue in dssp
file.
When I follow the same procedure for full protein molecule simulation I get
the same number of residue in dssp output as well as final.gro file
shahid nayeem
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

On 1/6/10 7:52 AM, leila karami wrote:

Hi
dear Justin
The executable is dssp
leila karami



Do you have the correct mode set for the executable (i.e., is it actually 
executable)?  Did you use a pre-compiled binary, or compile it yourself from 
source?  If you issue "which dssp" does your shell find the executable (again 
going back to potential PATH or environment issues)?


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp

[leila karami]

Hi

dear Justin

The executable is dssp

leila karami
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Re: [gmx-users] do_dssp

[Nuno Azoia]

Hi Leila!

Can I add just one more note?

The file dssp, that you put in the right place, has the permissions to
be executed?

Nuno Azoia

On Wed, 2010-01-06 at 15:35 +0330, leila karami wrote:
> dear Rasoul
>  
> I put executable DSSP in /usr/local/bin and gromacs is
> in /usr/local/gromacs.
>  
> is it true?
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-- 
Nuno Gonçalo Azoia Lopes
 
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Re: [gmx-users] do_dssp

[rasoul nasiri]

OK. you are right!

Rasoul

On Wed, Jan 6, 2010 at 1:09 PM, Justin A. Lemkul  wrote:

>
>
> On 1/6/10 7:05 AM, leila karami wrote:
>
>> dear Rasoul
>> I put executable DSSP in /usr/local/bin and gromacs is
>> in /usr/local/gromacs.
>> is it true?
>>
>>
> Is the executable named DSSP, or dssp?  Case matters.  DSSP is the
> environment variable that must be set, while dssp is the name of the
> executable itself.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] do_dssp

[rasoul nasiri]

yes. Could you perform do_dssp properly?

Rasoul


On Wed, Jan 6, 2010 at 1:05 PM, leila karami wrote:

> dear Rasoul
>
> I put executable DSSP in /usr/local/bin and gromacs is
> in /usr/local/gromacs.
>
> is it true?
>
> --
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

On 1/6/10 7:05 AM, leila karami wrote:

dear Rasoul
I put executable DSSP in /usr/local/bin and gromacs is
in /usr/local/gromacs.
is it true?



Is the executable named DSSP, or dssp?  Case matters.  DSSP is the environment 
variable that must be set, while dssp is the name of the executable itself.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp

[leila karami]

dear Rasoul

I put executable DSSP in /usr/local/bin and gromacs is
in /usr/local/gromacs.

is it true?
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

On 1/6/10 6:57 AM, rasoul nasiri wrote:

Then your executable has problem. Gromacs tool can not find DSSP for
doing d_dssp. Do you put executable DSSP in the path of gromacs is
installed?



This is not necessary.  One needs to set the environment variable DSSP 
correctly, since the default location that do_dssp expects is 
/usr/local/bin/dssp, not anything to do with the location of Gromacs.


-Justin


Rasoul.

On Wed, Jan 6, 2010 at 11:58 AM, leila karami mailto:karami.lei...@gmail.com>> wrote:

dear Rasoul
I had executable dssp program, already.
leila karami

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

On 1/6/10 5:58 AM, leila karami wrote:

dear Rasoul
I had executable dssp program, already.


Then have you set your PATH appropriately, as well as the DSSP environment 
variable?  See the help information for do_dssp to see the assumptions that the 
program is making regarding the location of the DSSP executable, as well as the 
numerous posts in the archive about this issue.


-Justin


leila karami



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[rasoul nasiri]

Then your executable has problem. Gromacs tool can not find DSSP for doing
d_dssp. Do you put executable DSSP in the path of gromacs is installed?

Rasoul.

On Wed, Jan 6, 2010 at 11:58 AM, leila karami wrote:

> dear Rasoul
>
> I had executable dssp program, already.
>
> leila karami
>
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[gmx-users] do_dssp

[leila karami]

dear Rasoul

I had executable dssp program, already.

leila karami
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Re: [gmx-users] do_dssp

[rasoul nasiri]

Do you have a DSSP program on your system? If no, please install executable
DSSP program from http://swift.cmbi.kun.nl/gv/dssp/ website.

Rasoul

On Wed, Jan 6, 2010 at 11:34 AM, leila karami wrote:

> Hi
>
> I apply following command:
>
> do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map
>
> but following error is came up:
>
> Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddal9qL4 ddRvmyo0 >
> /dev/null 2> /dev/null
>
>
> Any help will highly appreciated!
>
>
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[gmx-users] do_dssp

[leila karami]

Hi

I apply following command:

do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map

but following error is came up:

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddal9qL4 ddRvmyo0 >
/dev/null 2> /dev/null


Any help will highly appreciated!
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Re: [gmx-users] do_dssp Installation instructions in case you have errors

[Mark Abraham]

Kirill Bessonov wrote:
I had seen people having trouble with do_dssp and that Error line 471 
error.


Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 
2> /dev/null


So I would like to spill some light on the issue and make documentation 
better to understand after hours fiddling with source code.


Why did you spend hours looking at the source code? The documentation in 
do_dssp -h clearly specifies the need to set the executable name in the 
environment variable DSSP. The documentation and the error message upon 
non-existence of the path to DSSP could be improved such that it is not 
specific to C-shell.


If you have this error this means that dssp executable was not found 
even though the PATH was set correctly (i.e. DSSP path variable)


It's not a path variable - you've made a wrong assumption.

If you look at the source code the fexist funciton checks if there is 
any file in directory and returns true, so if you have any file there 
the code will run through and fail on line:


sprintf(dssp,"%s %s %s %s > /dev/null %s",
  dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null");

where dssp is the buffer of charcters and dptr is the pointer to the 
dssp executable file (not the folder!)



And that is the main source of errors, improper definition of directory 
pointer to the executable.


That's not the mistake. The "mistake" is GROMACS only checking for 
existence of the contents of DSSP and assuming the user has read the 
documentation. If the user erroneously specifies a path which exists, 
the check succeeds. It could/should check for existence, being 
executable, not being a directory, being non-zero size, not being a Unix 
virus, not being an alias for "sudo rm -rf /", etc. but one can't 
protect the user from everything :-)


Mark

Solution: To correct this mistake add to the path the name of the dssp 
exectutable.


E.g. if you named it dssp and put it in your home folder. Add to 
.bash_profile


DSSP=/home/dssp   (where dssp is not a FOLDER but name of executable)

If you named executable dsspmbi

DSSP=/home/dsspmbi   (and again dsspmbi is the name of executable)

This will define the location of dssp executable properly and you would 
not see any weird complicated errors coming up.


Hope it helps


 


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[gmx-users] do_dssp Installation instructions in case you have errors

[Kirill Bessonov]

I had seen people having trouble with do_dssp and that Error line 471 error.


Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro
/dev/null 2> /dev/null


So I would like to spill some light on the issue and make documentation
better to understand after hours fiddling with source code.

If you have this error this means that dssp executable was not found even
though the PATH was set correctly (i.e. DSSP path variable)

If you look at the source code the fexist funciton checks if there is any
file in directory and returns true, so if you have any file there the code
will run through and fail on line:

sprintf(dssp,"%s %s %s %s > /dev/null %s",
  dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null");

where dssp is the buffer of charcters and dptr is the pointer to the dssp
executable file (not the folder!)


And that is the main source of errors, improper definition of directory
pointer to the executable.

Solution: To correct this mistake add to the path the name of the dssp
exectutable.

E.g. if you named it dssp and put it in your home folder. Add to
.bash_profile

DSSP=/home/dssp   (where dssp is not a FOLDER but name of executable)

If you named executable dsspmbi

DSSP=/home/dsspmbi   (and again dsspmbi is the name of executable)

This will define the location of dssp executable properly and you would not
see any weird complicated errors coming up.

Hope it helps
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Re: [gmx-users] do_dssp question

[Justin A. Lemkul]

Kirill Bessonov wrote:
I have used do_dssp program to analyze secondary structure during 
simulation of DMPC/DMPE. But I am not clear on installation of dssp.


The program seems to work, I have set all the environmental variables so 
that dssp binary is seen in /home/DSSP directory, but I am not sure if I 
need to download the database of dssp files from the internet to make 
this program work.




No libraries or other databases are necessary.



There are 14 residues in your selected group
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
trn version: GMX_trn_file (single precision)
Reading frame   0 time   52.000  
Back Off! I just backed up ddoSxMLN to ./#ddoSxMLN.1#
Last frame  0 time   52.000  


100%

And I get ss.xps file that when I open it in image viewer is just a blue 
line.




Then you've got a consistently helical protein.  It could be that your axes are 
skewed a bit, but you can change proportions using a .m2p file.  An example is 
available in the online manual.


How should I properly setup the program and whether it will give me 
%alpha helicity over the course of the trajectory, thank you




To calculate % helicity, make use of scount.xvg (the other default output).

-Justin





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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp question

[Kirill Bessonov]

I have used do_dssp program to analyze secondary structure during simulation
of DMPC/DMPE. But I am not clear on installation of dssp.

The program seems to work, I have set all the environmental variables so
that dssp binary is seen in /home/DSSP directory, but I am not sure if I
need to download the database of dssp files from the internet to make this
program work.


There are 14 residues in your selected group
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
trn version: GMX_trn_file (single precision)
Reading frame   0 time   52.000
Back Off! I just backed up ddoSxMLN to ./#ddoSxMLN.1#
Last frame  0 time   52.000

100%

And I get ss.xps file that when I open it in image viewer is just a blue
line.

How should I properly setup the program and whether it will give me %alpha
helicity over the course of the trajectory, thank you
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Re: [gmx-users] do_dssp fatal error

[Justin A. Lemkul]

Homa Azizian wrote:

Hi
thanks Dr. van der Spoel my previous problem fixed.
I have another question.
I download DSSP from http://swift.cmbi.ru.nl/gv/dssp/ from the part 
Distribution in the left partition of the page. it was the zip file and I 
unzip it and positioned it in my /usr/local/bin and adjust the .bashrc. 
when I execut it the error appear:


Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro
/dev/null 2> /dev/null



The executable itself must be in /usr/local/bin.  If you placed the unzipped 
archive in /usr/local/bin, then dssp is a directory.  Furthermore, the 
executable produced from that source code will be call dsspcbmi, and will have 
to be re-named.


-Justin



How can I fix the problem?
Than's.


Tehran University of Medical Sciences
www.tums.ac.ir




--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp fatal error

[Homa Azizian]

Hi
thanks Dr. van der Spoel my previous problem fixed.
I have another question.
I download DSSP from http://swift.cmbi.ru.nl/gv/dssp/ from the part 
Distribution in the left partition of the page. it was the zip file and I 
unzip it and positioned it in my /usr/local/bin and adjust the .bashrc. 
when I execut it the error appear:

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro
/dev/null 2> /dev/null


How can I fix the problem?
Than's.


Tehran University of Medical Sciences
www.tums.ac.ir


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Re: [gmx-users] do_dssp fatal error

[Diego Enry Gomes]

Did you download the "dssp" software from here ?
http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi


On Mar 10, 2009, at 1:12 AM, Homa Azizian wrote:



Hi

when I use do_dssp the following error come:

Program do_dssp, VERSION 4.0.3
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro

/dev/null 2> /dev/null


How could I fix this.
Thank you in advance.
--
Tehran University of Medical Sciences
www.tums.ac.ir


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[gmx-users] do_dssp fatal error

[Homa Azizian]

Hi 

when I use do_dssp the following error come:

Program do_dssp, VERSION 4.0.3
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro 
> /dev/null 2> /dev/null

How could I fix this.
Thank you in advance. 
--
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www.tums.ac.ir


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Re: [gmx-users] do_dssp

[Mark Abraham]

Morteza Khabiri wrote:

Dear gmxuser,

I ried the do_dssp command to analyses my protein structure. It produce
scount.xvg ans ss.xpm file. I could see xvg file by xmgrace and ss,xpm by
GIMP software. Till now everything is ok. But when I want a make post
script file by xpm2ps for producing plot.eps file I get the following
error:
There are 1 matrices in ss.xpm
Matrix 0 is 954 x 290
Segmentation fault


Please be aware

a) this has nothing to do with GROMACS (and thus nothing to do with this 
list), because
b) a segmentation fault is an indication of a program failure that can 
have any conceivable cause, and
c) the problem arose in a utility that is not part of GROMACS when the 
input was known to work in a third-party tool (GIMP).


The most likely hypothesis is that your xpm2ps is not suitable for your 
architecture. If you can test it with some other input, that might give 
you useful information for diagnosis. The least likely hypothesis is 
that you've identified a problem in the way GROMACS (in do_dssp) writes 
a .xpm file.


Mark
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[gmx-users] do_dssp

[Morteza Khabiri]

Dear gmxuser,

I ried the do_dssp command to analyses my protein structure. It produce
scount.xvg ans ss.xpm file. I could see xvg file by xmgrace and ss,xpm by
GIMP software. Till now everything is ok. But when I want a make post
script file by xpm2ps for producing plot.eps file I get the following
error:
There are 1 matrices in ss.xpm
Matrix 0 is 954 x 290
Segmentation fault

What should be the fault.

thanks

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Re: [gmx-users] do_dssp

[Mark Abraham]

Morteza Khabiri wrote:

Dear florian
thanks for your help. I installed the DSSP in the root. It is working well
when I run ./dssp in DSSP directory. It seems that the program don't have
any problem. As you said I already set an environment also but any of them
did not working. It made me crazy that everything is ok, Installing the
dssp and also defenition of dssp directory but still i get the previous
message.


All we can guess is that you haven't done it right. If you want more 
help, we need more specific information, like what you actually did :-)


Mark
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[gmx-users] do_dssp

[Morteza Khabiri]

Dear florian
thanks for your help. I installed the DSSP in the root. It is working well
when I run ./dssp in DSSP directory. It seems that the program don't have
any problem. As you said I already set an environment also but any of them
did not working. It made me crazy that everything is ok, Installing the
dssp and also defenition of dssp directory but still i get the previous
message.

thanks

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Re: [gmx-users] do_dssp

[Florian Haberl]

Hi,
On Wednesday, 29. October 2008, Morteza Khabiri wrote:
> Dear gmx users,
>
> I run the program do_dssp for my system which is too small. Unfortunately,
> I run it for a long time but I am in a doubt that it is working correctly
> or not
> because it is run for one day and i don't have any idea when it will be
> finished and also after running I have a message which said "sh:
> /usr/local/bin/dssp: is a directory" Which take me in a doubt that do_dssp
>  run correctly or not.
>
> Please give me at least some idea about end time of program.

have you installed dssp?

do_dssp -h

do_dssp reads a trajectory file and computes the secondary structure for each
time frame calling the dssp program. If you do not have the dssp program, get
it. do_dssp assumes that the dssp executable is /usr/local/bin/dssp. If this
is not the case, then you should set an environment variable DSSP pointing to
the dssp executable, e.g.:

setenv DSSP /opt/dssp/bin/dssp


Greetings,

Florian 
-- 
---
 Dr. Florian Haberl
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
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[gmx-users] do_dssp

[Morteza Khabiri]

Dear gmx users,

I run the program do_dssp for my system which is too small. Unfortunately,
I run it for a long time but I am in a doubt that it is working correctly
or not
because it is run for one day and i don't have any idea when it will be
finished and also after running I have a message which said "sh:
/usr/local/bin/dssp: is a directory" Which take me in a doubt that do_dssp
 run correctly or not.

Please give me at least some idea about end time of program.

Thanks,




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Re: [gmx-users] do_dssp

[Nuno Azoia]

Maybe I can help with some more details. I'm sorry if my explanation is 
to much detailed.


I start to use do_dssp a few days ago. I went to the website Justin just 
mentioned and I just downloaded the binary file. I copy that file to 
/usr/local/bin
The binary file that I downloaded is dsspcmbi. So, before try do_dssp I 
create a soft link "dssp" to the binary dsspcmbi. I've created the link 
in the same directory (/usr/local/bin), and everything is just work fine.


Nuno Azoia



Justin A. Lemkul wrote:



minnale wrote:
 
Thanks for the reply Justin

I tried like this
do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str
it has given
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)



The prerequisite is a separate (non-Gromacs) program called DSSP.  It 
is available here:


http://swift.cmbi.ru.nl/gv/dssp/

Install dssp into /usr/local/bin and try do_dssp again.

-Justin

I checked with archives do_dssp is a seperate program and install 
separately,
Could you pls tell me how can I install do_dssp program or is there 
anyway to calculate  secondary structure of protein?

Thanks in advance.


On Fri, 15 Aug 2008 Justin A.Lemkul wrote :
 >
 >As a final note, it is probably better to use the .xtc file for 
analysis.  The do_dssp program is very slow, and I can only imagine 
that reading the full-precision trajectory will slow to an absolute 
crawl.

 >
 >-Justin
 >
 >Justin A. Lemkul wrote:
 >>
 >>
 >>minnale wrote:
 >>>  Hi all,
 >>>  I want to analyse secondary struture of my protein which have 
run MD for 7ns. I have checked in archives about do_dssp, found that 
can use only .pdb file instead of .trr and .tpr. Then if type command 
with -h it has it has given .xtc, .tpr,  and .ndx should use.

 >>
 >>Where does it say that you can't use your trajectory?  That's 
certainly incorrect.  The standalone dssp program (which you must 
obtain separately from the DSSP site) can only run on a single .pdb 
file, but Gromacs makes use of the dssp executable such that it can 
be used with trajectories.

 >>
 >>Hence the lovely plots you see in the literature.
 >>
 >>-Justin
 >>
 >>>I am bit confusing with about do_dssp command.
 >>>Can you explain me clearly. Thanks in advance.
 >>>
 >>>
 >>>
 >>>Rediff Shopping 
 



 >
 >Justin A. Lemkul
 >Graduate Research Assistant
 >Department of Biochemistry
 >Virginia Tech
 >Blacksburg, VA
 >jalemkul[at]vt.edu | (540) 231-9080
 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 >



Rediff Shopping 
 








--

Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal

Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293

Mobile: +351 965 382 487
E-mail: [EMAIL PROTECTED]

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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

minnale wrote:
 
Thanks for the reply Justin

I tried like this
do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str
it has given
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)



The prerequisite is a separate (non-Gromacs) program called DSSP.  It is 
available here:


http://swift.cmbi.ru.nl/gv/dssp/

Install dssp into /usr/local/bin and try do_dssp again.

-Justin

I checked with archives do_dssp is a seperate program and install 
separately,
Could you pls tell me how can I install do_dssp program or is there 
anyway to calculate  secondary structure of protein?

Thanks in advance.


On Fri, 15 Aug 2008 Justin A.Lemkul wrote :
 >
 >As a final note, it is probably better to use the .xtc file for 
analysis.  The do_dssp program is very slow, and I can only imagine that 
reading the full-precision trajectory will slow to an absolute crawl.

 >
 >-Justin
 >
 >Justin A. Lemkul wrote:
 >>
 >>
 >>minnale wrote:
 >>>  Hi all,
 >>>  I want to analyse secondary struture of my protein which have run 
MD for 7ns. I have checked in archives about do_dssp, found that can use 
only .pdb file instead of .trr and .tpr. Then if type command with -h it 
has it has given .xtc, .tpr,  and .ndx should use.

 >>
 >>Where does it say that you can't use your trajectory?  That's 
certainly incorrect.  The standalone dssp program (which you must obtain 
separately from the DSSP site) can only run on a single .pdb file, but 
Gromacs makes use of the dssp executable such that it can be used with 
trajectories.

 >>
 >>Hence the lovely plots you see in the literature.
 >>
 >>-Justin
 >>
 >>>I am bit confusing with about do_dssp command.
 >>>Can you explain me clearly. Thanks in advance.
 >>>
 >>>
 >>>
 >>>Rediff Shopping 
 


 >>>
 >>>
 >>>
 >>>
 >>>___
 >>>gmx-users mailing listgmx-users@gromacs.org
 >>>http://www.gromacs.org/mailman/listinfo/gmx-users
 >>>Please search the archive at http://www.gromacs.org/search before 
posting!
 >>>Please don't post (un)subscribe requests to the list. Use the www 
interface or send it to [EMAIL PROTECTED]

 >>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >>
 >
 >-- 
 >
 >Justin A. Lemkul
 >Graduate Research Assistant
 >Department of Biochemistry
 >Virginia Tech
 >Blacksburg, VA
 >jalemkul[at]vt.edu | (540) 231-9080
 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 >



Rediff Shopping 






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Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: Re: [gmx-users] do_dssp

[minnale]

  
Thanks for the reply Justin 
I tried like this 
do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str
it has given 
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)

I checked with archives do_dssp is a seperate program and install separately, 
Could you pls tell me how can I install do_dssp program or is there anyway to 
calculate  secondary structure of protein?
Thanks in advance. 


On Fri, 15 Aug 2008 Justin A.Lemkul wrote :
>
>As a final note, it is probably better to use the .xtc file for analysis.  The 
>do_dssp program is very slow, and I can only imagine that reading the 
>full-precision trajectory will slow to an absolute crawl.
>
>-Justin
>
>Justin A. Lemkul wrote:
>>
>>
>>minnale wrote:
>>>  Hi all,
>>>   I want to analyse secondary struture of my protein which have run MD for 
>>> 7ns. I have checked in archives about do_dssp, found that can use only .pdb 
>>> file instead of .trr and .tpr. Then if type command with -h it has it has 
>>> given .xtc, .tpr,  and .ndx should use.
>>
>>Where does it say that you can't use your trajectory?  That's certainly 
>>incorrect.  The standalone dssp program (which you must obtain separately 
>>from the DSSP site) can only run on a single .pdb file, but Gromacs makes use 
>>of the dssp executable such that it can be used with trajectories.
>>
>>Hence the lovely plots you see in the literature.
>>
>>-Justin
>>
>>>I am bit confusing with about do_dssp command.
>>>Can you explain me clearly. Thanks in advance.
>>>
>>>
>>>
>>>Rediff Shopping 
>>>>> PROTECTED]/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null> 
>>>
>>>
>>>
>>>
>>>___
>>>gmx-users mailing listgmx-users@gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/search before posting!
>>>Please don't post (un)subscribe requests to the list. Use the www interface 
>>>or send it to [EMAIL PROTECTED]
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

As a final note, it is probably better to use the .xtc file for analysis.  The 
do_dssp program is very slow, and I can only imagine that reading the 
full-precision trajectory will slow to an absolute crawl.


-Justin

Justin A. Lemkul wrote:



minnale wrote:
 
Hi all,
  I want to analyse secondary struture of my protein which have run MD 
for 7ns. I have checked in archives about do_dssp, found that can use 
only .pdb file instead of .trr and .tpr. Then if type command with -h 
it has it has given .xtc, .tpr,  and .ndx should use.


Where does it say that you can't use your trajectory?  That's certainly 
incorrect.  The standalone dssp program (which you must obtain 
separately from the DSSP site) can only run on a single .pdb file, but 
Gromacs makes use of the dssp executable such that it can be used with 
trajectories.


Hence the lovely plots you see in the literature.

-Justin


I am bit confusing with about do_dssp command.
Can you explain me clearly. Thanks in advance.



Rediff Shopping 
 






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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] do_dssp

[Justin A. Lemkul]

minnale wrote:
 
Hi all,
  I want to analyse secondary struture of my protein which have run MD 
for 7ns. I have checked in archives about do_dssp, found that can use 
only .pdb file instead of .trr and .tpr. Then if type command with -h it 
has it has given .xtc, .tpr,  and .ndx should use.


Where does it say that you can't use your trajectory?  That's certainly 
incorrect.  The standalone dssp program (which you must obtain separately from 
the DSSP site) can only run on a single .pdb file, but Gromacs makes use of the 
dssp executable such that it can be used with trajectories.


Hence the lovely plots you see in the literature.

-Justin


I am bit confusing with about do_dssp command.
Can you explain me clearly. 
Thanks in advance.




Rediff Shopping 






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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] do_dssp

[minnale]

  
Hi all, 
  I want to analyse secondary struture of my protein which have run MD for 7ns. 
I have checked in archives about do_dssp, found that can use only .pdb file 
instead of .trr and .tpr. Then if type command with -h it has it has given 
.xtc, .tpr,  and .ndx should use.
I am bit confusing with about do_dssp command.
Can you explain me clearly.  
Thanks in advance.___
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[gmx-users] do_dssp file format, Resolved !!!

[ABEL Stephane 175950]

Hi Gromacs Users 

My Problem with do_dssp is resolved : my do_dssp was strangely corrupted. After 
recompilation it works well. Thank you for all people who helped me. See U soon 
on this mailing list

Stefane
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Re: [gmx-users] do_dssp file format

[David van der Spoel]

ABEL Stephane 175950 wrote:

Yes, Mark i have taken a look in your previous message

To test my dssp program I took a pdb from the protein data bank: 1HRC. This pdb 
contains only one protein (and one frame). The DSSP program works fine with it 
and I obtain an output. So To test my do_dssp i also used this pdb. In this 
case when i choose MainChain 5 or other choices I obtain the same message 
described below and no output. I think, I have set correctly the DSSP 
environment variable because i have not the Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP). 
Moreover i think that ten minutes is not to short to process one config indeed 
the DSSP program take less than 2 seconds to compute the secondary structure of 
the protein in 1HRC pdb file.

So i very frustrated...

Stefane




so if you run

setenv DSSP `which dssp`
echo 1 | do_dssp -f 1HRC -s 1HRC

you get no output? do you have write permission in the work directory?

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] do_dssp file format

[ABEL Stephane 175950]

Yes, Mark i have taken a look in your previous message

To test my dssp program I took a pdb from the protein data bank: 1HRC. This pdb 
contains only one protein (and one frame). The DSSP program works fine with it 
and I obtain an output. So To test my do_dssp i also used this pdb. In this 
case when i choose MainChain 5 or other choices I obtain the same message 
described below and no output. I think, I have set correctly the DSSP 
environment variable because i have not the Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP). 
Moreover i think that ten minutes is not to short to process one config indeed 
the DSSP program take less than 2 seconds to compute the secondary structure of 
the protein in 1HRC pdb file.

So i very frustrated...

Stefane




ABEL Stephane 175950 wrote:
> Hi Gromacs users 
> 
> After many try this weekend with my problem with do_dssp I come back to the 
> mailing list  
> 
> First, as David said me last friday in a previous message I have test my dssp 
> program with example of pdb file from the Protein Data Bank (1HRC) (with one 
> protein configuration in it)
> 
> It works ! the calculation of the secondary structure is made and i obtain an 
> output. 
> 
> When i use this pdb with do_dssp with the following command 
> 
>  /applications/gromacs-3.3.2-fftw/bin/do_dssp -s test_template.pdb -f 
> test_template.pdb -o ss.xpm 
> 
> I obtain the menu and I choose 5 (MainChain) 
> 
> I obtained the follwing message:
> 
> There are 103 residues in your selected group
> Opening library file /applications/gromacs-3.3.2-fftw/share/gromacs/top/ss.map
> Reading frame   0 time   -1.000
> Back Off! I just backed up ddEG4D6s to ./#ddEG4D6s.1#
> 
> And the calculation is not made (I wait more than ten minutes) and i obtain 
> no ss.xpm 
> 
> I dont understand what is the problem

This could easily be too short a time if there are multiple frames in 
your pdb file. I don't know whether you have or need to follow the 
suggestion I made last time... 
http://www.gromacs.org/pipermail/gmx-users/2008-January/031720.html

Also, per "man do_dssp" you need to have set your DSSP environment 
variable correctly.

Finally, test do_dssp on the same .pdb file you say works with dssp.

Mark


--

Message: 2
Date: Mon, 14 Jan 2008 09:45:33 -0200
From: [EMAIL PROTECTED]
Subject: [gmx-users] grompp problem with trr input option
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain;   charset=ISO-8859-1; DelSp="Yes";
format="flowed"

Hi all

When I run grompp with a trr input file using the command line showed below

grompp -np 2 -t run_1.trr -f md_2 -p topol_2.top -o run_2

it gives me a error:

Program grompp, VERSION 3.3.1
Source code file: futil.c, line: 340

File input/output error:
conf.gro

Could anyone tell me how I can fix it?

Thank you in advance.

Sergio Garay
Biochemist
Facultad de Bioq. y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina




--

Message: 3
Date: Mon, 14 Jan 2008 12:59:31 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] grompp problem with trr input option
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

[EMAIL PROTECTED] wrote:
> Hi all
> 
> When I run grompp with a trr input file using the command line showed below
> 
> grompp -np 2 -t run_1.trr -f md_2 -p topol_2.top -o run_2
> 
> it gives me a error:
> 
> Program grompp, VERSION 3.3.1
> Source code file: futil.c, line: 340
> 
> File input/output error:
> conf.gro
> 
> Could anyone tell me how I can fix it?

you need to supply a conf as well. it will not be used.
> 
> Thank you in advance.
> 
> Sergio Garay
> Biochemist
> Facultad de Bioq. y Cs. Biológicas
> Universidad Nacional del Litoral
> Santa Fe - Argentina
> 
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww 
> interface or send it to [EMAIL PROTECTED]
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se


--

Message: 4
Date: Mon, 14 Jan 2008 08:44:04 -0800 (PST)
From: Mufaddal Soni <[EMAIL PROTECTED]>
Subject: [gmx-users] about details of the topology file.
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"

Dear users,
Thankyou for helping me regarding the topology file of my FNP 
inhibitor. I am facin

Re: [gmx-users] do_dssp file format

[Mark Abraham]

ABEL Stephane 175950 wrote:
Hi Gromacs users 

After many try this weekend with my problem with do_dssp I come back to the mailing list  


First, as David said me last friday in a previous message I have test my dssp 
program with example of pdb file from the Protein Data Bank (1HRC) (with one 
protein configuration in it)

It works ! the calculation of the secondary structure is made and i obtain an output. 

When i use this pdb with do_dssp with the following command 

 /applications/gromacs-3.3.2-fftw/bin/do_dssp -s test_template.pdb -f test_template.pdb -o ss.xpm 

I obtain the menu and I choose 5 (MainChain) 


I obtained the follwing message:

There are 103 residues in your selected group
Opening library file /applications/gromacs-3.3.2-fftw/share/gromacs/top/ss.map
Reading frame   0 time   -1.000
Back Off! I just backed up ddEG4D6s to ./#ddEG4D6s.1#

And the calculation is not made (I wait more than ten minutes) and i obtain no ss.xpm 


I dont understand what is the problem


This could easily be too short a time if there are multiple frames in 
your pdb file. I don't know whether you have or need to follow the 
suggestion I made last time... 
http://www.gromacs.org/pipermail/gmx-users/2008-January/031720.html


Also, per "man do_dssp" you need to have set your DSSP environment 
variable correctly.


Finally, test do_dssp on the same .pdb file you say works with dssp.

Mark
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[gmx-users] do_dssp file format

[ABEL Stephane 175950]

Hi Gromacs users 

After many try this weekend with my problem with do_dssp I come back to the 
mailing list  

First, as David said me last friday in a previous message I have test my dssp 
program with example of pdb file from the Protein Data Bank (1HRC) (with one 
protein configuration in it)

It works ! the calculation of the secondary structure is made and i obtain an 
output. 

When i use this pdb with do_dssp with the following command 

 /applications/gromacs-3.3.2-fftw/bin/do_dssp -s test_template.pdb -f 
test_template.pdb -o ss.xpm 

I obtain the menu and I choose 5 (MainChain) 

I obtained the follwing message:

There are 103 residues in your selected group
Opening library file /applications/gromacs-3.3.2-fftw/share/gromacs/top/ss.map
Reading frame   0 time   -1.000
Back Off! I just backed up ddEG4D6s to ./#ddEG4D6s.1#

And the calculation is not made (I wait more than ten minutes) and i obtain no 
ss.xpm 

I dont understand what is the problem

Thank you again for your help

Stefane


> Thanks Justin for your reply
>
> So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to test.
> I obtained always the same error.
>
> Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> Reading frame   0 time   -1.000
> Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#

What error?  It appears that do_dssp is backing up an old intermediate file that
gets generated as part of the calculation.

-Justin

>
> Note that the pdb seems correct because the secondary structure can be
> obtained with Stride available in VMD. And my trajectory was made CHARMM
> ffield. is this a problem in this case
>
> Thank a lot
>
> My story with do_dssp
>
> As suggested David and others i rename my pdb file with the extension .pdb
>
> i used the following command
>
> ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb
>
> A menu appears, I choose the group 1 (protein) and i obtained the error
> message
>
> Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> Reading frame   0 time   -1.000
> Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#
>
> What iis the problem. I give below a part of my pdb file
>
> ATOM  1 CAY  ACE 1   6.421  -7.877 -11.574 -0.27  0.00
> ATOM  2 HA1  ACE 1   6.050  -8.804 -12.062  0.09  0.00
> ATOM  3 HA2  ACE 1   6.728  -7.203 -12.402  0.09  0.00
> ATOM  4 HA3  ACE 1   5.529  -7.417 -11.098  0.09  0.00
> ATOM  5 CACE 1   7.470  -8.140 -10.510  0.51  0.00
> ATOM  6 OACE 1   7.594  -9.280 -10.074 -0.51  0.00
> ATOM  7 NGLY 2   8.125  -7.096 -10.030 -0.47  0.00
> ATOM  8 HN   GLY 2   7.927  -6.156 -10.295  0.31  0.00
> ATOM  9 CA   GLY 2   8.970  -7.131  -8.819 -0.02  0.00
> ATOM 10 HA1  GLY 2   8.889  -8.007  -8.193  0.09  0.00
> ATOM 11 HA2  GLY 2   8.638  -6.265  -8.265  0.09  0.00
> ATOM 12 CGLY 2  10.408  -6.734  -9.033  0.51  0.00
> ATOM 13 OGLY 2  11.313  -7.365  -8.492 -0.51  0.00
> ATOM 14 NASP 3  10.647  -5.532  -9.599 -0.47  0.00
> ATOM 15 HN   ASP 3   9.863  -5.073 -10.011  0.31  0.00
> ATOM 16 CA   ASP 3  11.864  -4.806  -9.831  0.07  0.00
> ATOM 17 HA   ASP 3  12.713  -5.321  -9.406  0.09  0.00
> ATOM 18 CB   ASP 3  12.026  -4.347 -11.282 -0.28  0.00
> ATOM 19 HB1  ASP 3  11.065  -4.008 -11.725  0.09  0.00
> ATOM 20 HB2  ASP 3  12.877  -3.652 -11.448  0.09  0.00
> ATOM 21 CG   ASP 3  12.414  -5.579 -12.163  0.62  0.00
> ATOM 22 OD1  ASP 3  11.641  -5.923 -13.130 -0.76  0.00
> ATOM 23 OD2  ASP 3  13.571  -5.997 -12.137 -0.76  0.00
>
> Thank you again for your kindly help
>
> Stefane
>
> ABEL Stephane 175950 wrote:
> > I used the following command
> >
> > ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a
> part is show below. I obtained a segmentation fault.
> >
> > Maybe it is not a the good command. Remember that my trajectories are not
> made/compatible with GROMACS and i have only a pdb coordinates of my MD.
> >
> don't rename the .pdb file to .tpr. Just use .pdb
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> [EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
>
>
> --
>
> Message: 2
> Date: Fri, 11 Jan 2008 09:30:47 +1100
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Re: Targeted MD
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Steven Kirk wrote:
> > Mark Abraham <[EMAIL PROTECTED]> wrote
>
> >> "Non-Protein" serves well here. So a usual tc-grps line has "Protein
> >> Non-Protein" for a pro

Re: [gmx-users] do_dssp file format

[Mark Abraham]

ABEL Stephane 175950 wrote:

I am back :(

The procedure i did

1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm
The menu appears I choose 5 (Main Chain) and I obtained the following message 


The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But the program seems to run because the prompt did not appear but the ouput ss.xpm is never present. 


What is the problem ?


http://wiki.gromacs.org/index.php/do_dssp

Mark
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Re: [gmx-users] do_dssp file format

[Justin A. Lemkul]

Is it a single structure in the .pdb file?  Or is it many frames of a
trajectory?  It is noted in the manual that do_dssp is very slow.  In my
experience (on my laptop), I can analyze 5 frames in roughly 3 hours.  Are
you waiting long enough for do_dssp to finish?

-Justin

Quoting ABEL Stephane 175950 <[EMAIL PROTECTED]>:

> I am back :(
>
> The procedure i did
>
> 1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm
> The menu appears I choose 5 (Main Chain) and I obtained the following message
> 
> GROningen MAchine for Chemical Simulation
>
> :-)  VERSION 3.3.1  (-:
>
>
>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2006, The GROMACS development team,
> check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
>  :-)  /applications/gromacs-3.3.1-fftw/bin/do_dssp  (-:
>
> Option Filename  Type Description
> 
>   -f test-Struc.pdb  InputGeneric trajectory: xtc trr trj gro g96 pdb
>   -s test-Struc.pdb  InputStructure+mass(db): tpr tpb tpa gro g96 pdb
>xml
>   -n  index.ndx  Input, Opt.  Index file
> -ssdump  ssdump.dat  Output, Opt. Generic data file
> -map ss.map  Input, Lib.  File that maps matrix data to colors
>   -o ss.xpm  Output   X PixMap compatible matrix file
>  -sc scount.xvg  Output   xvgr/xmgr file
>   -a   area.xpm  Output, Opt. X PixMap compatible matrix file
>  -tatotarea.xvg  Output, Opt. xvgr/xmgr file
>  -aa   averarea.xvg  Output, Opt. xvgr/xmgr file
>
>   Option   Type  Value  Description
> --
>   -[no]h   bool no  Print help info and quit
>   -[no]X   bool no  Use dialog box GUI to edit command line options
>-niceint 19  Set the nicelevel
>   -b   time  0  First frame (ps) to read from trajectory
>   -e   time  0  Last frame (ps) to read from trajectory
>  -dt   time  1  Only use frame when t MOD dt = first time (ps)
>  -tu   enum ps  Time unit: ps, fs, ns, us, ms or s
>   -[no]w   bool no  View output xvg, xpm, eps and pdb files
>-[no]xvgr   boolyes  Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -sss string   HEBT  Secondary structures for structure count
>
> Opening library file
> /applications/gromacs-3.3.1-fftw/share/gromacs/top/phbres.dat
> Opening library file
> /applications/gromacs-3.3.1-fftw/share/gromacs/top/aminoacids.dat
> Group 0 (  System) has  1674 elements
> Group 1 ( Protein) has  1623 elements
> Group 2 (   Protein-H) has   796 elements
> Group 3 ( C-alpha) has   101 elements
> Group 4 (Backbone) has   304 elements
> Group 5 (   MainChain) has   405 elements
> Group 6 (MainChain+Cb) has   494 elements
> Group 7 ( MainChain+H) has   405 elements
> Group 8 (   SideChain) has  1218 elements
> Group 9 ( SideChain-H) has   391 elements
> Group10 ( Prot-Masses) has  1623 elements
> Group11 ( Non-Protein) has51 elements
> Group12 ( HSD) has51 elements
> Group13 (   Other) has51 elements
>
> I select a group: 5
> Selected 5: 'MainChain'
> There are 102 residues in your selected group <--- OK for me
> Opening library file
> /applications/gromacs-3.3.1-fftw/share/gromacs/top/ss.map
> Reading frame   0 time   -1.000
> Back Off! I just backed up ddsGGvys to ./#ddsGGvys.1#
>
> The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But
> the program seems to run because the prompt did not appear but the ouput
> ss.xpm is never present.
>
> What is the problem ?
>
> Thank you
>
>
> > Thanks Justin for your reply
> >
> > So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to
> test.
> > I obtained always the same error.
> >
> > Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> > Reading frame   0 time   -1.000
> > Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#
>
> What error?  It appears that do_dssp is backing up an old intermediate file
> that
> gets generated as part of the calculation.
>
> -Justin
>
> >
> > Note that the pdb seems correct because the secondary structure can be
> > obtained with Stride available in VMD. And my trajectory was made CHARMM
> > ffield. is this a problem in this case
> >
> > Thank a lot
> >
> > My story with do_

Re: [gmx-users] do_dssp file format

[David van der Spoel]

ABEL Stephane 175950 wrote:

I am back :(

The procedure i did

1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm
The menu appears I choose 5 (Main Chain) and I obtained the following message 

try running normal dssp first

dssp pdbfile

to see if dssp works

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
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[gmx-users] do_dssp file format

[ABEL Stephane 175950]

I am back :(

The procedure i did

1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm
The menu appears I choose 5 (Main Chain) and I obtained the following message 

GROningen MAchine for Chemical Simulation

:-)  VERSION 3.3.1  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

 :-)  /applications/gromacs-3.3.1-fftw/bin/do_dssp  (-:

Option Filename  Type Description

  -f test-Struc.pdb  InputGeneric trajectory: xtc trr trj gro g96 pdb
  -s test-Struc.pdb  InputStructure+mass(db): tpr tpb tpa gro g96 pdb
   xml
  -n  index.ndx  Input, Opt.  Index file
-ssdump  ssdump.dat  Output, Opt. Generic data file
-map ss.map  Input, Lib.  File that maps matrix data to colors
  -o ss.xpm  Output   X PixMap compatible matrix file
 -sc scount.xvg  Output   xvgr/xmgr file
  -a   area.xpm  Output, Opt. X PixMap compatible matrix file
 -tatotarea.xvg  Output, Opt. xvgr/xmgr file
 -aa   averarea.xvg  Output, Opt. xvgr/xmgr file

  Option   Type  Value  Description
--
  -[no]h   bool no  Print help info and quit
  -[no]X   bool no  Use dialog box GUI to edit command line options
   -niceint 19  Set the nicelevel
  -b   time  0  First frame (ps) to read from trajectory
  -e   time  0  Last frame (ps) to read from trajectory
 -dt   time  1  Only use frame when t MOD dt = first time (ps)
 -tu   enum ps  Time unit: ps, fs, ns, us, ms or s
  -[no]w   bool no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   boolyes  Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-sss string   HEBT  Secondary structures for structure count

Opening library file 
/applications/gromacs-3.3.1-fftw/share/gromacs/top/phbres.dat
Opening library file 
/applications/gromacs-3.3.1-fftw/share/gromacs/top/aminoacids.dat
Group 0 (  System) has  1674 elements
Group 1 ( Protein) has  1623 elements
Group 2 (   Protein-H) has   796 elements
Group 3 ( C-alpha) has   101 elements
Group 4 (Backbone) has   304 elements
Group 5 (   MainChain) has   405 elements
Group 6 (MainChain+Cb) has   494 elements
Group 7 ( MainChain+H) has   405 elements
Group 8 (   SideChain) has  1218 elements
Group 9 ( SideChain-H) has   391 elements
Group10 ( Prot-Masses) has  1623 elements
Group11 ( Non-Protein) has51 elements
Group12 ( HSD) has51 elements
Group13 (   Other) has51 elements

I select a group: 5
Selected 5: 'MainChain'
There are 102 residues in your selected group <--- OK for me
Opening library file /applications/gromacs-3.3.1-fftw/share/gromacs/top/ss.map
Reading frame   0 time   -1.000
Back Off! I just backed up ddsGGvys to ./#ddsGGvys.1#

The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But the 
program seems to run because the prompt did not appear but the ouput ss.xpm is 
never present. 

What is the problem ?

Thank you 


> Thanks Justin for your reply
>
> So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to test.
> I obtained always the same error.
>
> Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> Reading frame   0 time   -1.000
> Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#

What error?  It appears that do_dssp is backing up an old intermediate file that
gets generated as part of the calculation.

-Justin

>
> Note that the pdb seems correct because the secondary structure can be
> obtained with Stride available in VMD. And my trajectory was made CHARMM
> ffield. is this a problem in this case
>
> Thank a lot
>
> My story with do_dssp
>
> As suggested David and others i rename my pdb file with the extension .pdb
>
> i used the following command
>
> ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb
>
> A menu appears, I choose the group 1 (protein) and i obtained the error
> message
>
> Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> Reading frame   0 time   -1.000
> Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#
>
> What iis the problem. I give below a part of my pdb file
>
> ATOM  1 CAY  A

Re: [gmx-users] do_dssp file format

[Justin A. Lemkul]

Quoting ABEL Stephane 175950 <[EMAIL PROTECTED]>:

> My story with do_dssp
>
continues...https://webmail.cea.fr/Exchange/Stephane.ABEL/Bo%C3%AEte%20de%20r%C3%A9ception/?Cmd=contents&Page=1
>  Boîte de réception
>
> As suggested David and others i rename my pdb file with the extension .pdb
>
> i used the following command
>
> ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb
>
> A menu appears, I choose the group 1 (protein) and i obtained the error
> message
>
> Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> Reading frame   0 time   -1.000
> Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#
>
> What iis the problem. I give below a part of my pdb file

I don't see any error message.  But you're not going to get any output that way.
 As I (and others) have posted to the list several times, use the group
'MainChain' for secondary structure calculations.  Check the archive for these
things, the answers are often there.

-Justin

>
> ATOM  1 CAY  ACE 1   6.421  -7.877 -11.574 -0.27  0.00
> ATOM  2 HA1  ACE 1   6.050  -8.804 -12.062  0.09  0.00
> ATOM  3 HA2  ACE 1   6.728  -7.203 -12.402  0.09  0.00
> ATOM  4 HA3  ACE 1   5.529  -7.417 -11.098  0.09  0.00
> ATOM  5 CACE 1   7.470  -8.140 -10.510  0.51  0.00
> ATOM  6 OACE 1   7.594  -9.280 -10.074 -0.51  0.00
> ATOM  7 NGLY 2   8.125  -7.096 -10.030 -0.47  0.00
> ATOM  8 HN   GLY 2   7.927  -6.156 -10.295  0.31  0.00
> ATOM  9 CA   GLY 2   8.970  -7.131  -8.819 -0.02  0.00
> ATOM 10 HA1  GLY 2   8.889  -8.007  -8.193  0.09  0.00
> ATOM 11 HA2  GLY 2   8.638  -6.265  -8.265  0.09  0.00
> ATOM 12 CGLY 2  10.408  -6.734  -9.033  0.51  0.00
> ATOM 13 OGLY 2  11.313  -7.365  -8.492 -0.51  0.00
> ATOM 14 NASP 3  10.647  -5.532  -9.599 -0.47  0.00
> ATOM 15 HN   ASP 3   9.863  -5.073 -10.011  0.31  0.00
> ATOM 16 CA   ASP 3  11.864  -4.806  -9.831  0.07  0.00
> ATOM 17 HA   ASP 3  12.713  -5.321  -9.406  0.09  0.00
> ATOM 18 CB   ASP 3  12.026  -4.347 -11.282 -0.28  0.00
> ATOM 19 HB1  ASP 3  11.065  -4.008 -11.725  0.09  0.00
> ATOM 20 HB2  ASP 3  12.877  -3.652 -11.448  0.09  0.00
> ATOM 21 CG   ASP 3  12.414  -5.579 -12.163  0.62  0.00
> ATOM 22 OD1  ASP 3  11.641  -5.923 -13.130 -0.76  0.00
> ATOM 23 OD2  ASP 3  13.571  -5.997 -12.137 -0.76  0.00
>
> Thank you again for your kindly help
>
> Stefane
>
> ABEL Stephane 175950 wrote:
> > I used the following command
> >
> > ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a
> part is show below. I obtained a segmentation fault.
> >
> > Maybe it is not a the good command. Remember that my trajectories are not
> made/compatible with GROMACS and i have only a pdb coordinates of my MD.
> >
> don't rename the .pdb file to .tpr. Just use .pdb
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> [EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
>
>
> --
>
> Message: 2
> Date: Fri, 11 Jan 2008 09:30:47 +1100
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Re: Targeted MD
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Steven Kirk wrote:
> > Mark Abraham <[EMAIL PROTECTED]> wrote
>
> >> "Non-Protein" serves well here. So a usual tc-grps line has "Protein
> >> Non-Protein" for a protein simulation.
> >>
> >> Mark
> >
> > A supplementary question.
> >
> > The tc-grps line can take predefined standard group names such as
> > 'System', 'Protein' and 'Non-Protein'.
> >
> > Does the 'Protein' group need to actually BE a protein, or are 'Protein'
> > and 'Non-Protein' really synonyms for
> > 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ?
>
> I haven't read the code or found any mention in the manual, but I expect
> that src/share/top/aminoacids.dat contains the names of any amino acids,
> and thus implicitly defines these groups.
>
> Mark
>
>
> --
>
> Message: 3
> Date: Fri, 11 Jan 2008 09:24:40 +0800
> From: "xuji"<[EMAIL PROTECTED]>
> Subject: [gmx-users] Asking help about PME
> To: "gmx-users@gromacs.org" 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="gb2312"
>
> Hi all gromacs users:
>
> I am digging into the PME method in gromacs. Can someone tell
> me what files have something to do with PME and the corresponding
> method FFT?
>
> Thanks!
> 
>
>
> Best wishes!
>
> Ji Xu
> Institute of Process Engineering
> Chinese Academy of Sciences
> P.O.Box 353, Beijing, 100080, China
> Tel: +86-10-826

[gmx-users] do_dssp file format

[ABEL Stephane 175950]

My story with do_dssp 
continues...https://webmail.cea.fr/Exchange/Stephane.ABEL/Bo%C3%AEte%20de%20r%C3%A9ception/?Cmd=contents&Page=1
 Boîte de réception 

As suggested David and others i rename my pdb file with the extension .pdb

i used the following command 

./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb

A menu appears, I choose the group 1 (protein) and i obtained the error message 

Opening library file /applications/gromacs-3.2.1/share/top/ss.map
Reading frame   0 time   -1.000
Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#

What iis the problem. I give below a part of my pdb file

ATOM  1 CAY  ACE 1   6.421  -7.877 -11.574 -0.27  0.00
ATOM  2 HA1  ACE 1   6.050  -8.804 -12.062  0.09  0.00
ATOM  3 HA2  ACE 1   6.728  -7.203 -12.402  0.09  0.00
ATOM  4 HA3  ACE 1   5.529  -7.417 -11.098  0.09  0.00
ATOM  5 CACE 1   7.470  -8.140 -10.510  0.51  0.00
ATOM  6 OACE 1   7.594  -9.280 -10.074 -0.51  0.00
ATOM  7 NGLY 2   8.125  -7.096 -10.030 -0.47  0.00
ATOM  8 HN   GLY 2   7.927  -6.156 -10.295  0.31  0.00
ATOM  9 CA   GLY 2   8.970  -7.131  -8.819 -0.02  0.00
ATOM 10 HA1  GLY 2   8.889  -8.007  -8.193  0.09  0.00
ATOM 11 HA2  GLY 2   8.638  -6.265  -8.265  0.09  0.00
ATOM 12 CGLY 2  10.408  -6.734  -9.033  0.51  0.00
ATOM 13 OGLY 2  11.313  -7.365  -8.492 -0.51  0.00
ATOM 14 NASP 3  10.647  -5.532  -9.599 -0.47  0.00
ATOM 15 HN   ASP 3   9.863  -5.073 -10.011  0.31  0.00
ATOM 16 CA   ASP 3  11.864  -4.806  -9.831  0.07  0.00
ATOM 17 HA   ASP 3  12.713  -5.321  -9.406  0.09  0.00
ATOM 18 CB   ASP 3  12.026  -4.347 -11.282 -0.28  0.00
ATOM 19 HB1  ASP 3  11.065  -4.008 -11.725  0.09  0.00
ATOM 20 HB2  ASP 3  12.877  -3.652 -11.448  0.09  0.00
ATOM 21 CG   ASP 3  12.414  -5.579 -12.163  0.62  0.00
ATOM 22 OD1  ASP 3  11.641  -5.923 -13.130 -0.76  0.00
ATOM 23 OD2  ASP 3  13.571  -5.997 -12.137 -0.76  0.00

Thank you again for your kindly help

Stefane

ABEL Stephane 175950 wrote:
> I used the following command 
>  
> ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a 
> part is show below. I obtained a segmentation fault. 
>  
> Maybe it is not a the good command. Remember that my trajectories are not 
> made/compatible with GROMACS and i have only a pdb coordinates of my MD.
>  
don't rename the .pdb file to .tpr. Just use .pdb

-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se


--

Message: 2
Date: Fri, 11 Jan 2008 09:30:47 +1100
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: Targeted MD
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Steven Kirk wrote:
> Mark Abraham <[EMAIL PROTECTED]> wrote

>> "Non-Protein" serves well here. So a usual tc-grps line has "Protein 
>> Non-Protein" for a protein simulation.
>>
>> Mark
> 
> A supplementary question.
> 
> The tc-grps line can take predefined standard group names such as 
> 'System', 'Protein' and 'Non-Protein'.
> 
> Does the 'Protein' group need to actually BE a protein, or are 'Protein' 
> and 'Non-Protein' really synonyms for 
> 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ?

I haven't read the code or found any mention in the manual, but I expect 
that src/share/top/aminoacids.dat contains the names of any amino acids, 
and thus implicitly defines these groups.

Mark


--

Message: 3
Date: Fri, 11 Jan 2008 09:24:40 +0800
From: "xuji"<[EMAIL PROTECTED]>
Subject: [gmx-users] Asking help about PME
To: "gmx-users@gromacs.org" 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="gb2312"

Hi all gromacs users:

I am digging into the PME method in gromacs. Can someone tell
me what files have something to do with PME and the corresponding
method FFT? 
 
Thanks!



Best wishes!

Ji Xu
Institute of Process Engineering
Chinese Academy of Sciences
P.O.Box 353, Beijing, 100080, China
Tel: +86-10-82627076
Fax:+86-10-62558065
[EMAIL PROTECTED]

2008-01-11

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Message: 4
Date: Fri, 11 Jan 2008 13:10:11 +1100
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Asking help about PME
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; chars

Re: [gmx-users] do_dssp file format

[David van der Spoel]

ABEL Stephane 175950 wrote:
I used the following command 
 
./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. 
 
Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD.
 

don't rename the .pdb file to .tpr. Just use .pdb

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] do_dssp file format

[ABEL Stephane 175950]

I used the following command 
 
./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part 
is show below. I obtained a segmentation fault. 
 
Maybe it is not a the good command. Remember that my trajectories are not 
made/compatible with GROMACS and i have only a pdb coordinates of my MD.
 
 
Any help will be appreciate
 
Stefane
 
 
ATOM  1 CAY  ACE 1   6.421  -7.877 -11.574 -0.27  0.00
ATOM  2 HA1  ACE 1   6.050  -8.804 -12.062  0.09  0.00
ATOM  3 HA2  ACE 1   6.728  -7.203 -12.402  0.09  0.00
ATOM  4 HA3  ACE 1   5.529  -7.417 -11.098  0.09  0.00
ATOM  5 CACE 1   7.470  -8.140 -10.510  0.51  0.00
ATOM  6 OACE 1   7.594  -9.280 -10.074 -0.51  0.00
ATOM  7 NGLY 2   8.125  -7.096 -10.030 -0.47  0.00
ATOM  8 HN   GLY 2   7.927  -6.156 -10.295  0.31  0.00
ATOM  9 CA   GLY 2   8.970  -7.131  -8.819 -0.02  0.00
ATOM 10 HA1  GLY 2   8.889  -8.007  -8.193  0.09  0.00
ATOM 11 HA2  GLY 2   8.638  -6.265  -8.265  0.09  0.00
ATOM 12 CGLY 2  10.408  -6.734  -9.033  0.51  0.00
ATOM 13 OGLY 2  11.313  -7.365  -8.492 -0.51  0.00
ATOM 14 NASP 3  10.647  -5.532  -9.599 -0.47  0.00
ATOM 15 HN   ASP 3   9.863  -5.073 -10.011  0.31  0.00
ATOM 16 CA   ASP 3  11.864  -4.806  -9.831  0.07  0.00
ATOM 17 HA   ASP 3  12.713  -5.321  -9.406  0.09  0.00
ATOM 18 CB   ASP 3  12.026  -4.347 -11.282 -0.28  0.00
ATOM 19 HB1  ASP 3  11.065  -4.008 -11.725  0.09  0.00
ATOM 20 HB2  ASP 3  12.877  -3.652 -11.448  0.09  0.00
ATOM 21 CG   ASP 3  12.414  -5.579 -12.163  0.62  0.00
ATOM 22 OD1  ASP 3  11.641  -5.923 -13.130 -0.76  0.00
ATOM 23 OD2  ASP 3  13.571  -5.997 -12.137 -0.76  0.00

 
 
 
 
 
 
 



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Message: 3
Date: Thu, 10 Jan 2008 13:03:30 -0500
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] do_dssp file format
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1

Quoting ABEL Stephane 175950 <[EMAIL PROTECTED]>:

> > Hi gromacs users
> >
> > For my work I have performed some simulations of a protein in water with an
> other MD software not compatible with >GROMACS. And I would like to compute
> the time evolution of the secondary structure of my protein, I know that the
> >with >the xpm2ps tool give in gromacs. Is it possible to have an (small)
> exemple of an .xpm file generated by the do_dssp >tools
>
> Just run a 10-step MD simulation and generate one yourself. Or convert
> your other trajectories into .pdb format and use that as input to
> do_dssp. You do not necessarily need a .tpr file for do_dssp, see "man
> do_dssp" under the "-s" flag.
>
> Mark
>
> Thanks Mark for your suggestions but it is not working for me So i have
> tested an other approach with VMD to obtain the secondary structure time
> series for my protein. The ouput graph obtained is not pretty, so i would
> like to make for a paper a same graph that i found in some gromacs papers.
> For this i need to convert the output datas file of VMD to gromacs xpm file
> obtained with do_dssp with a script and convert it to ps with the xpm2ps
> tool. In gromacs documentation i can not find an exemple of xpm file
> generated with do_dssp. So it is possible to obtain from the gromacs users a
> small exemple of this file to see how the datas are arranged

What exactly is "not working?"  As in, what commands are you issuing?  Did the
MD fail, or the analysis of the trajectory?  If you provide this type of
information, we may be able to help you better.

-Justin

>
> Thank you very much
>
> Stefane
> ___
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>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/




--

Message: 4
Date: Thu, 10 Jan 2008 19:27:38 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Dihedral with parameters set to zero
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
C