Something went wrong. For details check last_carma_run.log located in

[Ruikang Yuan]

Hi,All:

when i tied to run my first grcarma.i met the problem ------Something went wrong. For details check last_carma_run.log located in 

i checked the mail listing and there is a solution you guys provided,but this is my fisrt time to use the tool,there is not an old version carma.

It is so weird that although the program feedbacks the fault , i can still get the data(for example ,Second Structure and gr).

then i tried to solve the problem by the following step, but it did not work:

i replaced the carma by carma64(my laptop is based on ubuntu18 x64)in the folder - /usr/local/bin，then i ran grcarma64 ,

the screen showed :Can't exec "carma": No such file or directory at script/grcarma.pl line 385.

Use of uninitialized value in pattern match (m//) at script/grcarma.pl line 385.

so i am curious why the foler i download has five programs (cluster5d grcarma64 grcarma carma64 carma),but the grcarma64 does not match with carma64? 

please help me! Thank you guys.

[Nicholas Glykos]

It is impossible to guess what is happening without additional info.

[1] Rename carma64 to carma in /usr/local/bin

[2] You don't really need grcarma64, all big matrices are handled by carma.
So run

grcarma my.dcd my.psf

and send me the contents of the last_carma_run.log


Alternatively, prepare a small DCD (with catDCD) and send the small DCD+PSF
so that we can reproduce the issue.

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--

Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/

[Ruikang Yuan]

thanks your reply.

i don't know what's going on...

NOW,when i launch grcarma in terminal

it  shows:

Usage: /tmp/par-connor/cache-eef133467d4ffd5efa9b83ec402fa33a5f232663/carma [ -Alib.par ] [ -Idir ] [ -Mmodule ] [ src.par ] [ program.pl ]
       /tmp/par-connor/cache-eef133467d4ffd5efa9b83ec402fa33a5f232663/carma [ -B|-b ] [-Ooutfile] src.par

 I delete the carma in /tmp/par-connor/cache-eef133467d4ffd5efa9b83ec402fa33a5f232663/,but the situation does not change.

[Nicholas M. Glykos]

Which operating system are you using ? These message come from PAR
(https://metacpan.org/pod/PAR) and I have not see them again.


Two things to try

[1] Delete the PAR directory in tmp and try again to run grcarma

rm -rf /tmp/par-connor/


[2] If you are on a mac os x machine, try a newer grcarma executable :

cd
wget https://utopia.duth.gr/glykos/progs/grcarma/macosx_grcarma_new
chmod 755 macosx_grcarma_new
sudo cp macosx_grcarma_new /usr/local/bin/grcarma

[Yuan Ruikang]

My system is ubuntu18.04.3lts.I deleted the /tmp/par-connor/,and I use grcarma and

 carma in /use/local/bin

it did work!

but when I load psf/dcd(from the vmd case study,it’s absolutely right ),the program shows”number of atoms in psf and dcd do not match .would you like to retry “

RuiKang Yuan

 

---

发件人: Nicholas M. Glykos <gly...@mbg.duth.gr>
发送时间: 星期二, 十一月 12, 2019 4:53 下午
收件人: Ruikang Yuan
抄送: Nicholas Glykos; carma molecular dynamics
主题: Re: [carma] Something went wrong. For details check last_carma_run.log located in

 

[Nicholas M. Glykos]

> My system is ubuntu18.04.3lts.I deleted the /tmp/par-connor/,and I use
> grcarma and
> carma in /use/local/bin it did work!

OK.

> but when I load psf/dcd(from the vmd case study,it’s absolutely right ),
> the program shows”number of atoms in psf and dcd do not match .would you
> like to retry “

I would bet that carma is right and that indeed the number of atoms in the
DCD and PSF files are not the same. Send a link so that I can download the
DCD+PSF files and test it, but my guess is that you either you are trying
to mix different pairs of DCD/PSF files.

[Nicholas M. Glykos]

Ha !! Nice catch. I can reproduce the issue. The stand alone carma
executable works nicely with this DCD+PSF, grcarma erroneously complains.

If you are in a hurry, you can use carma for now, until I sort this out.

Thanks.




On Tue, Nov 12, 2019 at 06:43:10PM +0800, Ruikang Yuan wrote:
> there are two files from VMD case study about Myoglobin.
> co-after500ps.dcd
>
> heme-co-ws.psf

[Nicholas M. Glykos]

OK, found it. The problem is this : your system contains only one
protein residue (with only one CA atom). When grcarma starts makes a quick
check that the DCD/PSF pair indeed contains a protein structure. This test
fails because it is based on checking that the system contains at least
two CA atoms.

I can fix that if you want to work with a system containing just one amino
acid. If your real system is a proper protein, you can continue with your
real calculations.

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[Ruikang Yuan]

It is not necessary to fix it.NOW,I turn to my research work,but the wrong log  is still there, I will send you the relative files.

It seems carma works well and I get the second strcuture.

 IMG_4776.JPG

 

Nicholas M. Glykos <gly...@mbg.duth.gr> 于2019年11月12日周二 下午8:41写道：

[Nicholas M. Glykos]

> It is not necessary to fix it.NOW,I turn to my research work,but the wrong
> log is still there, I will send you the relative files.
> It seems carma works well and I get the second strcuture.

The DCD is only 201 frames, so do send me links for the files (DCD+PSF) to
debug it.

[Nicholas M. Glykos]

I have a suspicion though : people are actively changing the flags for
gnome-terminal and this may break things.

Try this :

sudo apt install xterm

and try again with grcarma (and also check that grcarma uses xterm and not
gnome-terminal).

[Yuan Ruikang]

I am not in the lab.I will try it tomorrow and feedback the result to you.Thanks again！

RuiKang Yuan

 

---

发件人: Nicholas M. Glykos <gly...@mbg.duth.gr>

发送时间: 星期二, 十一月 12, 2019 11:27 下午
收件人: Ruikang Yuan
抄送: carma molecular dynamics

主题: Re: [carma] Something went wrong. For details check last_carma_run.log located in

 

[Yuan Ruikang]

I install xterm in my ubuntu.

And I input xterm in my gnome-terminal then another terminal opens.

I input grcarma in the new window.everything is fine!The “view results”button can be clicked.

Thanks!!!

 

---

发件人: Nicholas M. Glykos <gly...@mbg.duth.gr>

发送时间: 星期二, 十一月 12, 2019 11:27 下午
收件人: Ruikang Yuan
抄送: carma molecular dynamics

主题: Re: [carma] Something went wrong. For details check last_carma_run.log located in