Discussion:
dssp on PC
(too old to reply)
dastmalchi.s
1970-01-01 00:00:00 UTC
Permalink
Dear GMX users,

I have recently posted my problem regarding the installation of Gromacs on
sgi computer, but haven't got any reply yet. I will appreciate it if any
one could kindly reply to my previous question.

But for now, I was wondering if anyone has used the dssp under gromacs in
a PC computer running WinXP. I have done every thing that I could have
think of, but still the programs stops and says that
.....
The system cannot find the path specified.

After the above message, it hangs and I can see from the task manager that
dssp.exe is running but cannot find what it is looking for.
I don't know which path it refers to.

I will appreciate it if you let me know how I can fix this problem.

Cheer, Siavoush
Wang Zhun
2006-01-24 15:23:18 UTC
Permalink
Hi,
I'm not sure about using DSSP in WinXP, but you'd better check your environmental variables in your PC.
Right click "My computer" icon in your desktop, select "property", then "advanced" and "environmental variables".Make sure dssp.exe is in the "environmental variables" pathway.
Hope it helps.


Wang Zhun
From: <dastmalchi.s at tbzmed.ac.ir>
Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
To: <gmx-users at gromacs.org>
Subject: [gmx-users] dssp on PC
Date:Tue, 24 Jan 2006 19:09:38 -0300 (GMT+3)
Dear GMX users,
I have recently posted my problem regarding the installation of Gromacs on
sgi computer, but haven't got any reply yet. I will appreciate it if any
one could kindly reply to my previous question.
But for now, I was wondering if anyone has used the dssp under gromacs in
a PC computer running WinXP. I have done every thing that I could have
think of, but still the programs stops and says that
.....
The system cannot find the path specified.
After the above message, it hangs and I can see from the task manager that
dssp.exe is running but cannot find what it is looking for.
I don't know which path it refers to.
I will appreciate it if you let me know how I can fix this problem.
Cheer, Siavoush
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
dastmalchi.s
1970-01-01 00:00:00 UTC
Permalink
Dear Wang,

Many thanks for the suggestion, but I have already set the environmental
variable for dssp.exe and all other paths for the bin and top directories
were defined.

I don't know what else I need to look for.

Many thanks,
Siavoush
Post by Wang Zhun
Hi,
I'm not sure about using DSSP in WinXP, but you'd better check your
environmental variables in your PC. Right click "My computer" icon in
your desktop, select "property", then "advanced" and "environmental
variables".Make sure dssp.exe is in the "environmental variables"
pathway. Hope it helps.
Wang Zhun
From: <dastmalchi.s at tbzmed.ac.ir>
<gmx-users at gromacs.org>
Subject: [gmx-users] dssp on PC
Date:Tue, 24 Jan 2006 19:09:38 -0300 (GMT+3)
Dear GMX users,
I have recently posted my problem regarding the installation of Gromacs
on sgi computer, but haven't got any reply yet. I will appreciate it if
any one could kindly reply to my previous question.
But for now, I was wondering if anyone has used the dssp under gromacs
in a PC computer running WinXP. I have done every thing that I could
have think of, but still the programs stops and says that
.....
The system cannot find the path specified.
After the above message, it hangs and I can see from the task manager
that dssp.exe is running but cannot find what it is looking for.
I don't know which path it refers to.
I will appreciate it if you let me know how I can fix this problem.
Cheer, Siavoush
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Mark Abraham
2006-01-25 23:02:20 UTC
Permalink
Post by dastmalchi.s
Dear Wang,
Many thanks for the suggestion, but I have already set the environmental
variable for dssp.exe and all other paths for the bin and top directories
were defined.
Have you read the man page for do_dssp?

Mark
Dastmalchi
2006-01-26 08:20:15 UTC
Permalink
Hi,

DSSP alone is working fine. I did a search in Gromacs Search page and
realized that other people have already raised the same problem. Still I
couldn't find a solution to my problem.
I have downloaded the dssp for Windows from
http://swift.cmbi.ru.nl/gv/dssp/.
I guess do_dssp is not being directed to the location of the dssp
executable. I am not sure but my feeling was that if I set the following
environment variable,
set dssp=c:\dssp\DSSPCMBI.exe
and put the dssp directory in the path then issuing the dssp command from
anywhere should locate the executable file.
Thanks for your kind attention.

Cheers, Siavoush
Hi, Siavoush,
It's interesting that my email box did not receive your reply until I
browsed the GMX mailing list today.
You may first make sure DSSP works itself, so I suggest you carry out DSSP
to calculate the secondary structure of a known structure from PDB databank.
Regards,
Wang Zhun
Christoph Weise
2006-01-26 14:35:05 UTC
Permalink
One thing I noticed trying out dssp on XP (binary from
http://swift.cmbi.ru.nl/gv/dssp/) is that it is very
quiet so the source of trouble is difficult to trace.
In my case I found some downloaded pdb's were missing
a critical "MODEL" line and dssp was therefore not
returning output.

As for the path problem, I did it the easy/hard way: I
called dssp from within MATLAB with full filenames
including paths.

The recommended approach on the dssp webpage,

dsspcmbi source.pdb destination.dssp >messages.txt

doesn't seem to write messages.txt

Christoph
Post by Dastmalchi
Hi,
DSSP alone is working fine. I did a search in
Gromacs Search page and
realized that other people have already raised the
same problem. Still I
couldn't find a solution to my problem.
I have downloaded the dssp for Windows from
http://swift.cmbi.ru.nl/gv/dssp/.
I guess do_dssp is not being directed to the
location of the dssp
executable. I am not sure but my feeling was that if
I set the following
environment variable,
set dssp=c:\dssp\DSSPCMBI.exe
and put the dssp directory in the path then issuing
the dssp command from
anywhere should locate the executable file.
Thanks for your kind attention.
Cheers, Siavoush
Hi, Siavoush,
It's interesting that my email box did not receive
your reply until I
browsed the GMX mailing list today.
You may first make sure DSSP works itself, so I
suggest you carry out DSSP
to calculate the secondary structure of a known
structure from PDB databank.
Regards,
Wang Zhun
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the
list. Use the
www interface or send it to
gmx-users-request at gromacs.org.
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dastmalchi.s
1970-01-01 00:00:00 UTC
Permalink
Dear Wang,

Many thanks for your kind email. I used to use GMX on my O2 sgi machine
but she did while ago and recently I have got an other one. I was trying
to install GMX on my O2 but come across some problem so WinXP was a quick
alternative. In my installation of GMX on sgi I see many strange things,
and don't know if it is the latest version of the program which has got
the problem or it is my computer.
last time that I was trying to install it I was getting an ERROR message
saying that:
ERROR File = ghat.c, line 233
A value of type "int" cannot assigned to an entity of type "real ***"
gh = mk_rgrid (ix,iy,iz);
1 error detected in compilation of "ghat.c".


Today the problem is that it says, cannot find the fftw.h or dfftw.h, but
I have already installed FFTW both in single and double precision form,
and also I am using CPPFLAGS and LDFLAGS to let it know the location of
the lib and include directories.
I am going to do every thing from the beginning to see what happens.

Cheers, Siavoush
Ooh, I'm sorry I cann't help you. But why not try Linux version of GMX?
I once tried MS Windows version of GMX in Win2000 but came to many
problems, and gave it up at last.
Regards,
Wang Zhun
From: <dastmalchi.s at tbzmed.ac.ir>
To: <wangzhun at pumc.edu.cn>
Subject: Re: dssp on PC
Date:Fri, 27 Jan 2006 15:31:56 -0300 (GMT+3)
Hi Wang,
I called it dssp.exe, but it didn't make any diference.
Thanks,
Siavoush
What about changing DSSPCMBI.exe to DSSP.exe?
From: "Dastmalchi" <dastmalchi.s at tbzmed.ac.ir>
To: "gmx-users" <gmx-users at gromacs.org>,
"Wang Zhun " <wangzhun at pumc.edu.cn>
Subject: Re: dssp on PC
Date:Thu, 26 Jan 2006 11:50:15 +0330
Hi,
DSSP alone is working fine. I did a search in Gromacs Search page
and realized that other people have already raised the same
problem. Still I couldn't find a solution to my problem.
I have downloaded the dssp for Windows from
http://swift.cmbi.ru.nl/gv/dssp/.
I guess do_dssp is not being directed to the location of the dssp
executable. I am not sure but my feeling was that if I set the
following environment variable,
set dssp=c:\dssp\DSSPCMBI.exe
and put the dssp directory in the path then issuing the dssp
command from anywhere should locate the executable file.
Thanks for your kind attention.
Cheers, Siavoush
Hi, Siavoush,
It's interesting that my email box did not receive your reply
until
I
browsed the GMX mailing list today.
You may first make sure DSSP works itself, so I suggest you carry
out DSSP
to calculate the secondary structure of a known structure from PDB
databank.
Regards,
Wang Zhun
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