Re: [gmx-users] Re: do_dssp

2012-04-05 Thread Mark Abraham 
 
 
On 05/04/12, bharat gupta  wrote:

> Ok now after downloading the latest version of dssp,

 
This won't work, because the latest version of DSSP is newer than any released 
version of GROMACS, and they made big changes. This was discussed at length on 
the list only yesterday... go and find that thread to see how you need to 
proceed. 
 

>  and giving right permissions and after executing the /usr/local/bin/dssp 
> command I am getting the following output :-
> 
> [root@BHARATPC peptide2]# /usr/local/bin/dssp 

 
By running this program as root, you trusted it not to have a bug that could 
trash your computer. There is no reason to run that risk.
 
Mark 

> 
> 
> DSSP options:
>   -h [ --help ] Display help message
>   -i [ --input ] argInput file
>   -o [ --output ] arg   Output file, use 'stdout' to output to screen
>   -v [ --verbose ]  Verbose output
>   -d [ --debug ] argDebug level (for even more verbose output)
> 
> 
> Examples: 
> 
> To calculate the secondary structure for the file 1crn.pdb and
> write the result to a file called 1crn.dssp, you type:
> 
>   dssp.exe -i 1crn.pdb -o 1crn.dssp
> 
> 
> 
> 
> On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham  wrote:
> 
> 
> > 
> > 
> > On 5/04/2012 5:16 PM, bharat gupta wrote: 
> > 
> > 
> > > This is the output  :
> > > 
> > > [root@BHARATPC ~]# /usr/local/bin/dssp
> > > 
> > 
> > 
> > Don't run as root except for installing software, unless you like 
> > rebuilding your computer from the ground up.
> > 
> > 
> > 
> > > bash: /usr/local/bin/dssp: Permission denied
> > > 
> > 
> > Possibly you didn't give execute permission on some file or other. This is 
> > not a GROMACS problem, but rather a problem with how you have done your 
> > dssp installation. Consult its documentation.
> > 
> > 
> > 
> > 
> > > 
> > > I have already set the pat for dssp in .bashrc using export command , I 
> > > don't know why this error is there. Is it due to renaming dsspcmbi to 
> > > dssp ??
> > > 
> > 
> > 
> > You have now reported testing a command different from the one you reported 
> > that you had instructed do_dssp to use. So it is hard for me to believe 
> > your assertion that you are following the advice in do_dssp -h correctly 
> > with a correct version of DSSP.
> > 
> > 
> > 
> > Mark
> > 
> > 
> > 
> > > 
> > > 
> > > 
> > > On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham  
> > > wrote:
> > > 
> > > 
> > > > 
> > > > 
> > > > On 5/04/2012 4:16 PM, bharat gupta wrote: 
> > > > 
> > > > > Yes , I am using the correct options for dssp. But still I am getting 
> > > > > the same error. 
> > > > > 
> > > > 
> > > > 
> > > > What does invoking /usr/local/bin/dsspcmbi say?
> > > > 
> > > > Mark 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > > 
> > > > > 
> > > > > On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham 
> > > > >  wrote:
> > > > > 
> > > > > 
> > > > > > 
> > > > > > 
> > > > > > On 5/04/2012 10:25 AM, bharat gupta wrote:
> > > > > > 
> > > > > > 
> > > > > > > Hi,
> > > > > > > 
> > > > > > > I am trying to plot the ss content using the do_dssp command , 
> > > > > > > but I am getting the following error :-
> > > > > > > 
> > > > > > > Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn 
> > > > > > > ddXN9mH0 > /dev/null 2> /dev/null
> > > > > > > 
> > > > > > > I am using the DSSPold version. What could be the possible reason 
> > > > > > > for such an error ??
> > > > > > > 
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > Many of them. Start by making sure you're following the advice of 
> > > > > > do_dssp -h.
> > > > > > 
> > > > > > Mark 
> > > > > > 
> > > > > > 
> > > > > > -- 
> > > > > > 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
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > -- 
> > > > > Bharat
> > > > > Ph.D. Candidate
> > > > > Room No. : 7202A, 2nd Floor
> > > > > Biomolecular Engineering Laboratory
> > > > > Division of Chemical Engineering and Polymer Science
> > > > > Pusan National University
> > > > > Busan -609735
> > > > > South Korea
> > > > > Lab phone no. - +82-51-510-3680, +82-51-583-8343 
> > > > > Mobile no. - 010-5818-3680
> > > > > E-mail : monu46...@yahoo.com
> > > > > 
> > > > > 
> > > > > 
> > > > >  
> > > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > --
> > > > 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 requ

Re: [gmx-users] Re: do_dssp

2012-04-05 Thread bharat gupta 
Ok now after downloading the latest version of dssp, and giving right
permissions and after executing the /usr/local/bin/dssp command I am
getting the following output :-

[root@BHARATPC peptide2]# /usr/local/bin/dssp
DSSP options:
  -h [ --help ] Display help message
  -i [ --input ] argInput file
  -o [ --output ] arg   Output file, use 'stdout' to output to screen
  -v [ --verbose ]  Verbose output
  -d [ --debug ] argDebug level (for even more verbose output)


Examples:

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

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



On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham wrote:

>  On 5/04/2012 5:16 PM, bharat gupta wrote:
>
> *This is the output  :
>
> [root@BHARATPC ~]# /usr/local/bin/dssp
> *
>
>
> Don't run as root except for installing software, unless you like
> rebuilding your computer from the ground up.
>
> *bash: /usr/local/bin/dssp: Permission denied
> *
>
>
> Possibly you didn't give execute permission on some file or other. This is
> not a GROMACS problem, but rather a problem with how you have done your
> dssp installation. Consult its documentation.
>
>
> *
> I have already set the pat for dssp in .bashrc using export command , I
> don't know why this error is there. Is it due to renaming dsspcmbi to dssp
> ??
> *
>
>
> You have now reported testing a command different from the one you
> reported that you had instructed do_dssp to use. So it is hard for me to
> believe your assertion that you are following the advice in do_dssp -h
> correctly with a correct version of DSSP.
>
>
> Mark
>
> * *
>
> On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham wrote:
>
>>  On 5/04/2012 4:16 PM, bharat gupta wrote:
>>
>> Yes , I am using the correct options for dssp. But still I am getting the
>> same error.
>>
>>
>>  What does invoking /usr/local/bin/dsspcmbi say?
>>
>> Mark
>>
>>
>>
>> On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham wrote:
>>
>>>  On 5/04/2012 10:25 AM, bharat gupta wrote:
>>>
 Hi,

 I am trying to plot the ss content using the do_dssp command , but I am
 getting the following error :-

 Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn
 ddXN9mH0 > /dev/null 2> /dev/null

 I am using the DSSPold version. What could be the possible reason for
 such an error ??

>>>
>>>  Many of them. Start by making sure you're following the advice of
>>> do_dssp -h.
>>>
>>> Mark
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.com
>>
>>
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
>
>
>
>
>
> --
> 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
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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

Re: [gmx-users] Re: do_dssp

2012-04-05 Thread Mark Abraham 

On 5/04/2012 5:16 PM, bharat gupta wrote:

/This is the output  :

[root@BHARATPC ~]# /usr/local/bin/dssp
/


Don't run as root except for installing software, unless you like 
rebuilding your computer from the ground up.



/bash: /usr/local/bin/dssp: Permission denied
/


Possibly you didn't give execute permission on some file or other. This 
is not a GROMACS problem, but rather a problem with how you have done 
your dssp installation. Consult its documentation.



/
I have already set the pat for dssp in .bashrc using export command , 
I don't know why this error is there. Is it due to renaming dsspcmbi 
to dssp ??

/


You have now reported testing a command different from the one you 
reported that you had instructed do_dssp to use. So it is hard for me to 
believe your assertion that you are following the advice in do_dssp -h 
correctly with a correct version of DSSP.


Mark


//

On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham > wrote:


On 5/04/2012 4:16 PM, bharat gupta wrote:

Yes , I am using the correct options for dssp. But still I am
getting the same error.


What does invoking /usr/local/bin/dsspcmbi say?

Mark




On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:

On 5/04/2012 10:25 AM, bharat gupta wrote:

Hi,

I am trying to plot the ss content using the do_dssp
command , but I am getting the following error :-

Failed to execute command: /usr/local/bin/dsspcmbi -na
ddldj5Bn ddXN9mH0 > /dev/null 2> /dev/null

I am using the DSSPold version. What could be the
possible reason for such an error ??


Many of them. Start by making sure you're following the
advice of do_dssp -h.

Mark

-- 
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




-- 
Bharat

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 






--
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




--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 





-- 
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

Re: [gmx-users] Re: do_dssp

2012-04-05 Thread bharat gupta 
*This is the output  :

[root@BHARATPC ~]# /usr/local/bin/dssp
bash: /usr/local/bin/dssp: Permission denied

I have already set the pat for dssp in .bashrc using export command , I
don't know why this error is there. Is it due to renaming dsspcmbi to dssp
??
*

On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham wrote:

>  On 5/04/2012 4:16 PM, bharat gupta wrote:
>
> Yes , I am using the correct options for dssp. But still I am getting the
> same error.
>
>
> What does invoking /usr/local/bin/dsspcmbi say?
>
> Mark
>
>
>
> On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham wrote:
>
>>  On 5/04/2012 10:25 AM, bharat gupta wrote:
>>
>>> Hi,
>>>
>>> I am trying to plot the ss content using the do_dssp command , but I am
>>> getting the following error :-
>>>
>>> Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0
>>> > /dev/null 2> /dev/null
>>>
>>> I am using the DSSPold version. What could be the possible reason for
>>> such an error ??
>>>
>>
>>  Many of them. Start by making sure you're following the advice of
>> do_dssp -h.
>>
>> Mark
>>
>> --
>> 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
>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
>
>
>
>
>
> --
> 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
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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

Re: [gmx-users] Re: do_dssp

2012-04-05 Thread Mark Abraham 

On 5/04/2012 4:16 PM, bharat gupta wrote:
Yes , I am using the correct options for dssp. But still I am getting 
the same error.


What does invoking /usr/local/bin/dsspcmbi say?

Mark



On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham > wrote:


On 5/04/2012 10:25 AM, bharat gupta wrote:

Hi,

I am trying to plot the ss content using the do_dssp command ,
but I am getting the following error :-

Failed to execute command: /usr/local/bin/dsspcmbi -na
ddldj5Bn ddXN9mH0 > /dev/null 2> /dev/null

I am using the DSSPold version. What could be the possible
reason for such an error ??


Many of them. Start by making sure you're following the advice of
do_dssp -h.

Mark

-- 
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




--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 





-- 
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

Re: [gmx-users] Re: do_dssp

2012-04-04 Thread bharat gupta 
Yes , I am using the correct options for dssp. But still I am getting the
same error.

On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham wrote:

> On 5/04/2012 10:25 AM, bharat gupta wrote:
>
>> Hi,
>>
>> I am trying to plot the ss content using the do_dssp command , but I am
>> getting the following error :-
>>
>> Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0
>> > /dev/null 2> /dev/null
>>
>> I am using the DSSPold version. What could be the possible reason for
>> such an error ??
>>
>
> Many of them. Start by making sure you're following the advice of do_dssp
> -h.
>
> Mark
>
> --
> 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/Searchbefore
>  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
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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

Re: [gmx-users] Re: do_dssp

2012-04-04 Thread Mark Abraham 

On 5/04/2012 10:25 AM, bharat gupta wrote:

Hi,

I am trying to plot the ss content using the do_dssp command , but I 
am getting the following error :-


Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn 
ddXN9mH0 > /dev/null 2> /dev/null


I am using the DSSPold version. What could be the possible reason for 
such an error ??


Many of them. Start by making sure you're following the advice of 
do_dssp -h.


Mark
--
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

[gmx-users] Re: do_dssp

2012-04-04 Thread bharat gupta 
Hi,

I am trying to plot the ss content using the do_dssp command , but I am
getting the following error :-

Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 >
/dev/null 2> /dev/null

I am using the DSSPold version. What could be the possible reason for such
an error ??


Regards

-- 
Bharat
-- 
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

Re: [gmx-users] Re: do_dssp error

2012-03-30 Thread Mark Abraham 

On 30/03/2012 10:28 PM, Erik Marklund wrote:
And I replied "What's your dssp version? The most recent ones have 
different flags that are not yet supported by gromacs."




... and I asked whether you'd read and followed the advice in do_dssp 
-h. Asking for more help without appearing to have used that you've 
already received doesn't show much respect for the time people have 
already given. Where's their incentive to keep helping you? :-)


Mark


Erik

30 mar 2012 kl. 13.23 skrev Albert:


Hello:
 there is some problem for my do_dssp, it always claimed:

Program do_dssp_d, VERSION 4.5.5
Source code file: do_dssp.c, line: 572
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddg1g7Id ddRwthIi 
> /dev/null 2> /dev/null



someone suggest to compile gromacs with double precision and I 
recompiled it with --enable-double

but it still doesn't work.

does anybody else have any suggestions?

THX
--
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


---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se 
http://www2.icm.uu.se/molbio/elflab/index.html





-- 
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

Re: [gmx-users] Re: do_dssp error

2012-03-30 Thread Erik Marklund 
And I replied "What's your dssp version? The most recent ones have different 
flags that are not yet supported by gromacs."

Erik

30 mar 2012 kl. 13.23 skrev Albert:

> Hello:
>  there is some problem for my do_dssp, it always claimed:
> 
> Program do_dssp_d, VERSION 4.5.5
> Source code file: do_dssp.c, line: 572
> Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddg1g7Id ddRwthIi > 
> /dev/null 2> /dev/null
> 
> 
> someone suggest to compile gromacs with double precision and I recompiled it 
> with --enable-double
> but it still doesn't work.
> 
> does anybody else have any suggestions?
> 
> THX
> -- 
> 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

---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

-- 
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

[gmx-users] Re: do_dssp error

2012-03-30 Thread Albert 

Hello:
  there is some problem for my do_dssp, it always claimed:

Program do_dssp_d, VERSION 4.5.5
Source code file: do_dssp.c, line: 572
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddg1g7Id ddRwthIi > 
/dev/null 2> /dev/null



someone suggest to compile gromacs with double precision and I 
recompiled it with --enable-double

but it still doesn't work.

does anybody else have any suggestions?

THX
--
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