Re: [gmx-users] dssp

Justin A. Lemkul Fri, 05 Nov 2010 06:55:28 -0700


#ZHAO LINA# wrote:

But right now I noticed something a bit funny,

Try different times,

Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1#

-------------------------------------------------------
Program do_dssp, VERSION 4.0.7
Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471

Fatal error:
Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy > 
/dev/null 2> /dev/null


Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz > /dev/null 
2> /dev/null
Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax > /dev/null 
2> /dev/null
Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k > /dev/null 2> 
/dev/null

was something wrong with mine DSSP, except path reason.

I still think you're setting your DSSP environment variable wrong. Pleaseconsult the link I posted before - you have to point DSSP to the *actualexecutable* not the directory that contains it, i.e.:


WRONG: export DSSP=/opt/bin

RIGHT: export DSSP=/opt/bin/dssp

-Justin

Thanks,

lina
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Friday, November 05, 2010 9:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] dssp

Hi,

1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the "real and 
true" path to a simple way as it showed "pathTo..." before I posted.

2. seems not about root things, cause every body can write and read to/from 
/dev/null

3. I will try another time ?!

Thanks,

lina
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp

Linus Östberg wrote:

What did you try to do? To use dssp, you must select entire residues,
e.g. 1 (protein). That error sounds a bit like my problem when trying
to do dssp using only the backbone.


The original message indicates the wrong executable was called.  The reasons
might still be unclear at this point, but instead of executing "dssp," do_dssp
was executing "pathToDSSP" instead.

The group for analysis is also debatable.  I have seen hangs and seg faults when
"Protein" is selected, and other times it works fine.  The only absolute
requirement is that (at least) all "MainChain" atoms be considered.  The latest
version of GROMACS seems to handle "Protein" just fine, but older versions did
not.  I have no explanation for that, however :)

-Justin

// Linus Östberg

On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# <zhao0...@e.ntu.edu.sg> wrote:

Hi,

Thanks for your response, I modified that path parts when I posted that 
information.

So my environment set was correct.

I just suddenly realize I may not have root privilege there, cause the dssp was 
not small, not in mine personal computer, there are in some other places.

lina

________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp

#ZHAO LINA# wrote:

Hi,

Program do_dssp, VERSION 4.0.7
Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471

Fatal error:
Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null
2> /dev/null

It came out two or three file like  ddEPI6I2 and then died like above.

My first time try dssp, so do not know how to examine it.

Your DSSP environment variable is set incorrectly.  do_dssp is trying to call
"pathToDSSP" as the executable.

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

Note that you should substitute a meaningful PATH on your system, not something
like "pathToDSSP."

-Justin

Thanks for any advice,

lina

--
========================================

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 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
--
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


--
========================================

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 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
--
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


--
========================================

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 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 thewww interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] dssp

Reply via email to