schneiderfelipe commented 9 years ago

When I run $ ./auto_martini --smi "N1=C(N)NN=C1N" --mol GUA (taken from the documentation), I receive the following on Ubuntu 15.04 64bits:

;;;; GENERATED WITH auto-martini
; INPUT SMILES: N1=C(N)NN=C1N
; Tristan Bereau (2014)

[moleculetype]
; molname       nrexcl
  GUA           2

[atoms]
; id    type    resnr   residu  atom    cgnr    charge  smiles
  1     SP2     1       GUA     S01     1       0     ; Nc1ncnn1
  2     SP2     1       GUA     S02     2       0     ; Nc1ncnn1

[constraints]
;  i   j     funct   length
   1   2     1       0.21

python: /usr/include/boost/thread/pthread/mutex.hpp:108: boost::mutex::~mutex(): Assertion `!posix::pthread_mutex_destroy(&m)' failed.
[1]    31433 abort (core dumped)  ./auto_martini --smi "N1=C(N)NN=C1N" --mol GUA

What am I doing wrong?

Best regards, Felipe Schneider

tbereau commented 9 years ago

Hi Felipe,

I haven't been able to reproduce this error on any of my machines, but apparently the boost library is not able to properly close the multiple processes (pthreads) on your machine when the code finishes. I'm not sure why that is, but may have to do with strange interactions between RDKit and Boost. In any event, that happens only when the program closes, so any of the results you get aren't affected. I'll keep you posted if I find out more.

Best, Tristan

glosar commented 9 years ago

Hi Tristan, I would like to use auto_martini so I installed it with all the dependencies required. When I try to run it, on benzene or n-butane for example, I receive the following error:

$ ./auto_martini --smi "CCCC" --mol NBUT Traceback (most recent call last): File "./auto_martini", line 1203, in ringAtomsFlat, True)

Any help is welcome, best regards

Gloria

tbereau commented 9 years ago

Hi Gloria,

I can't reproduce your error message. Which python version are you using? Maybe you could try with a different python version, or even within ipython (if you have it). In the ipython's command line:

%run auto_martini --smi "CCCC" --mol NBUT

Does that provide a more detailed error message?

Best, Tristan

glosar commented 9 years ago

Dear Tristan, thank you for your reply.

I have recently installed the CentOS7 on my workstation and the python version as read from print(sys.version) is:

2.7.5 (default, Jun 24 2015, 00:41:19) [GCC 4.8.3 20140911 (Red Hat 4.8.3-9)]

yum info also gives the following details:

Name : python Arch : x86_64 Version : 2.7.5 Release : 18.el7_1.1

May be that I need of another version?

Regards, Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Wed, 16 Sep 2015 23:12:59 -0700 Tristan Bereau notifications@github.com wrote:

Hi Gloria,

I can't reproduce your error message. Which python version are you using? Maybe you could try with a different python version, or even within ipython (if you have it). In the ipython's command line:
%run auto_martini --smi "CCCC" --mol NBUT
Does that provide a more detailed error message?

Best, Tristan

Reply to this email directly or view it on GitHub: https://github.com/tbereau/auto_martini/issues/1#issuecomment-140978184

tbereau commented 9 years ago

Dear Gloria,

Python 2.7.5 is just fine. What's puzzling me is the lack of information in the error message, there's usually a bit more about what's causing problems.

Do you happen to have ipython, or any other version of python, installed as well? Does it give you the same error message?

You can also try an alternative branch, see if you get the same error:

git checkout refactor
python auto_martini.py --smi "CCCC" --mol NBUT

Let me know what happens.

Best, Tristan

On Thu, Sep 17, 2015 at 9:05 AM, glosar notifications@github.com wrote:

Dear Tristan, thank you for your reply.

I have recently installed the CentOS7 on my workstation and the python version as read from print(sys.version) is:

2.7.5 (default, Jun 24 2015,

00:41:19) [GCC 4.8.3 20140911 (Red Hat 4.8.3-9)]

yum info also gives the following details:

Name : python Arch : x86_64 Version : 2.7.5 Release : 18.el7_1.1

May be that I need of another version?

Regards, Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Wed, 16 Sep 2015 23:12:59 -0700 Tristan Bereau notifications@github.com wrote:
Hi Gloria,

I can't reproduce your error message. Which python version are you using? Maybe you could try with a different python version, or even within ipython (if you have it). In the ipython's command line:
%run auto_martini --smi "CCCC" --mol NBUT
Does that provide a more detailed error message?

Best, Tristan

Reply to this email directly or view it on GitHub: https://github.com/tbereau/auto_martini/issues/1#issuecomment-140978184
— Reply to this email directly or view it on GitHub https://github.com/tbereau/auto_martini/issues/1#issuecomment-140988156.

glosar commented 9 years ago

Typing python followed by tab key I find: python python2 python2.7 python2.7-config python2-config python-config

All of them are located in /usr/bin and running diff command any difference appears. Also sys.version gives the same result. yum install info answers only about python giving the details reported in the previous email.

Can I do something else?

Thanks,

Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Thu, 17 Sep 2015 00:31:16 -0700 Tristan Bereau notifications@github.com wrote:

Dear Gloria,

Python 2.7.5 is just fine. What's puzzling me is the lack of information in the error message, there's usually a bit more about what's causing problems.

Do you happen to have ipython, or any other version of python, installed as well? Does it give you the same error message?

You can also try an alternative branch, see if you get the same error:
git checkout refactor
python auto_martini.py --smi "CCCC" --mol NBUT
Let me know what happens.

Best, Tristan

On Thu, Sep 17, 2015 at 9:05 AM, glosar notifications@github.com wrote:
Dear Tristan, thank you for your reply.

I have recently installed the CentOS7 on my workstation and the python version as read from print(sys.version) is:

2.7.5 (default, Jun 24 2015,

00:41:19) [GCC 4.8.3 20140911 (Red Hat 4.8.3-9)]

yum info also gives the following details:

Name : python Arch : x86_64 Version : 2.7.5 Release : 18.el7_1.1

May be that I need of another version?

Regards, Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Wed, 16 Sep 2015 23:12:59 -0700 Tristan Bereau notifications@github.com wrote:
Hi Gloria,

I can't reproduce your error message. Which python version are you using? Maybe you could try with a different python version, or even within ipython (if you have it). In the ipython's command line:
%run auto_martini --smi "CCCC" --mol NBUT
Does that provide a more detailed error message?

Best, Tristan

Reply to this email directly or view it on GitHub:

https://github.com/tbereau/auto_martini/issues/1#issuecomment-140978184
— Reply to this email directly or view it on GitHub https://github.com/tbereau/auto_martini/issues/1#issuecomment-140988156.
Reply to this email directly or view it on GitHub: https://github.com/tbereau/auto_martini/issues/1#issuecomment-140992005

tbereau commented 9 years ago

Dear Gloria,

Without an explicit error message it's difficult to guess what's going on. Maybe you could try installing a different version of python (e.g., 3.0) and see whether the same error comes back, and if so, whether you get a more explicit error message.

Best, Tristan

On Thu, Sep 17, 2015 at 9:53 AM, glosar notifications@github.com wrote:

Typing python followed by tab key I find: python python2 python2.7 python2.7-config python2-config python-config

All of them are located in /usr/bin and running diff command any difference appears. Also sys.version gives the same result. yum install info answers only about python giving the details reported in the previous email.

Can I do something else?

Thanks,

Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Thu, 17 Sep 2015 00:31:16 -0700

Tristan Bereau notifications@github.com wrote:
Dear Gloria,

Python 2.7.5 is just fine. What's puzzling me is the lack of information in the error message, there's usually a bit more about what's causing problems.

Do you happen to have ipython, or any other version of python, installed as well? Does it give you the same error message?

You can also try an alternative branch, see if you get the same error:
git checkout refactor
python auto_martini.py --smi "CCCC" --mol NBUT
Let me know what happens.

Best, Tristan

On Thu, Sep 17, 2015 at 9:05 AM, glosar notifications@github.com wrote:
Dear Tristan, thank you for your reply.

I have recently installed the CentOS7 on my workstation and the python version as read from print(sys.version) is:

2.7.5 (default, Jun 24 2015,

00:41:19) [GCC 4.8.3 20140911 (Red Hat 4.8.3-9)]

yum info also gives the following details:

Name : python Arch : x86_64 Version : 2.7.5 Release : 18.el7_1.1

May be that I need of another version?

Regards, Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Wed, 16 Sep 2015 23:12:59 -0700 Tristan Bereau notifications@github.com wrote:
Hi Gloria,

I can't reproduce your error message. Which python version are you using? Maybe you could try with a different python version, or even within ipython (if you have it). In the ipython's command line:
%run auto_martini --smi "CCCC" --mol NBUT
Does that provide a more detailed error message?

Best, Tristan

Reply to this email directly or view it on GitHub:

https://github.com/tbereau/auto_martini/issues/1#issuecomment-140978184
— Reply to this email directly or view it on GitHub < https://github.com/tbereau/auto_martini/issues/1#issuecomment-140988156>.
Reply to this email directly or view it on GitHub: https://github.com/tbereau/auto_martini/issues/1#issuecomment-140992005
— Reply to this email directly or view it on GitHub https://github.com/tbereau/auto_martini/issues/1#issuecomment-140995355.

glosar commented 9 years ago

Dear Tristan, I resolved using python3 on auto_martini.py

Thank you for your help!

I have another question: I've seen in the code that the heavy atoms limit is 25, so I tried to submit the SMCC (24 heavy atoms) molecule (smile: C1CC(CCC1CN2C(=O)C=CC2=O)C(=O)ON3C(=O)CCC3=O). Unfortunately even if the process starts and runs without giving any error, in few minutes it falls in D state any output is produced. Have you some hint about it?

Regards, Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Thu, 17 Sep 2015 04:26:57 -0700 Tristan Bereau notifications@github.com wrote:

Dear Gloria,

Without an explicit error message it's difficult to guess what's going on. Maybe you could try installing a different version of python (e.g., 3.0) and see whether the same error comes back, and if so, whether you get a more explicit error message.

Best, Tristan

On Thu, Sep 17, 2015 at 9:53 AM, glosar notifications@github.com wrote:
Typing python followed by tab key I find: python python2 python2.7 python2.7-config python2-config python-config

All of them are located in /usr/bin and running diff command any difference appears. Also sys.version gives the same result. yum install info answers only about python giving the details reported in the previous email.

Can I do something else?

Thanks,

Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Thu, 17 Sep 2015 00:31:16 -0700

Tristan Bereau notifications@github.com wrote:
Dear Gloria,

Python 2.7.5 is just fine. What's puzzling me is the lack of information in the error message, there's usually a bit more about what's causing problems.

Do you happen to have ipython, or any other version of python, installed as well? Does it give you the same error message?

You can also try an alternative branch, see if you get the same error:
git checkout refactor
python auto_martini.py --smi "CCCC" --mol 
NBUT
Let me know what happens.

Best, Tristan

On Thu, Sep 17, 2015 at 9:05 AM, glosar notifications@github.com wrote:
Dear Tristan, thank you for your reply.

I have recently installed the CentOS7 on my workstation and the python version as read from print(sys.version) is:

2.7.5 (default, Jun 24 2015,

00:41:19) [GCC 4.8.3 20140911 (Red Hat 4.8.3-9)]

yum info also gives the following details:

Name : python Arch : x86_64 Version : 2.7.5 Release : 18.el7_1.1

May be that I need of another version?

Regards, Gloria

Gloria Anna Ada Saracino PhD

Center of Nanomedicine and Tissue Engineering (CNTE) A.O. Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore 3 Milan, 20162, Italy

tel. +39 02 64447527 fax. +39 02 87073821

Università degli Studi di Milano-Bicocca Dipartimento di Biotecnologie e Bioscienze Piazza della Scienza 2 Milan, 20126, Italy

tel. +39 02 6448 3312 fax. +39 02 6448 3314 On Wed, 16 Sep 2015 23:12:59 -0700 Tristan Bereau notifications@github.com wrote:
Hi Gloria,

I can't reproduce your error message. Which python version are you using? Maybe you could try with a different python version, or even within ipython (if you have it). In the ipython's command line:
%run auto_martini --smi "CCCC" --mol NBUT
Does that provide a more detailed error message?

Best, Tristan

Reply to this email directly or view it on GitHub:

https://github.com/tbereau/auto_martini/issues/1#issuecomment-140978184
— Reply to this email directly or view it on GitHub < https://github.com/tbereau/auto_martini/issues/1#issuecomment-140988156>.
Reply to this email directly or view it on GitHub:

https://github.com/tbereau/auto_martini/issues/1#issuecomment-140992005
— Reply to this email directly or view it on GitHub https://github.com/tbereau/auto_martini/issues/1#issuecomment-140995355.
Reply to this email directly or view it on GitHub: https://github.com/tbereau/auto_martini/issues/1#issuecomment-141048829

tbereau commented 9 years ago

Dear Gloria,

Very glad Python 3 resolved the first issue.

It may be that the error you get is due to memory limitations on your machine. I've ran the code on that Smiles string. Here's the output:

mol.itp

; GENERATED WITH auto_martini.py ; None ; Tristan Bereau (2014)

[moleculetype] ; molname nrexcl MOL 2

[atoms] ; id type resnr residue atom cgnr charge smiles 1 SC2 1 MOL S01 1 0 ; [C]1[C][C][C][C][C]1 2 SC2 1 MOL S02 2 0 ; [C]1[C][C][C][C][C]1 3 SC1 1 MOL S03 3 0 ; [C][C]1[C][C][C][C][C]1 4 SP2 1 MOL S04 4 0 ; O=C1[C]=[C][C][N]1 5 SP2 1 MOL S05 5 0 ; O=C1[C]=[C][C][N]1 6 P2 1 MOL P01 6 0 ; [N]O[C]=O 7 SP2 1 MOL S06 7 0 ; O=C1[C][C][C][N]1 8 SP2 1 MOL S07 8 0 ; O=C1[C][C][C][N]1

[bonds] ; i j funct length force.c. 1 6 1 0.31 1250 3 5 1 0.36 1250 6 8 1 0.25 1250

[constraints] ; i j funct length 1 2 1 0.26 1 3 1 0.26 2 3 1 0.26 4 5 1 0.22 7 8 1 0.23

[angles] ; i j k funct angle force.c. 1 3 5 2 98.6 25.0 1 6 8 2 147.2 45.0 2 1 6 2 65.2 25.0 2 3 5 2 158.3 25.0 3 1 6 2 101.3 25.0 3 5 4 2 62.5 45.0 6 8 7 2 63.8 45.0

[dihedrals] ; i j k l funct angle force.c. 1 2 3 4 2 -142.7 10.0 1 3 2 6 2 -52.1 10.0 1 6 2 3 2 48.7 10.0 2 1 3 4 2 167.2 10.0 2 3 1 6 2 52.1 10.0 2 6 1 3 2 -48.4 10.0 3 1 2 6 2 121.6 10.0 3 2 1 6 2 -121.6 10.0

atomistic.gro

MOL generated from auto_martini.py 24 1MOL C 1 0.054 -0.127 -0.189 2MOL C 2 -0.089 -0.082 -0.155 3MOL C 3 -0.163 -0.189 -0.073 4MOL C 4 -0.070 -0.269 0.022 5MOL C 5 0.054 -0.187 0.062 6MOL C 6 0.140 -0.149 -0.061 7MOL C 7 0.227 -0.026 -0.028 8MOL N 8 0.327 -0.003 -0.132 9MOL C 9 0.444 -0.079 -0.160 10MOL O 10 0.473 -0.187 -0.103 11MOL C 11 0.525 -0.012 -0.261 12MOL C 12 0.464 0.101 -0.294 13MOL C 13 0.342 0.111 -0.216 14MOL O 14 0.260 0.206 -0.221 15MOL C 15 -0.276 -0.126 0.004 16MOL O 16 -0.395 -0.157 -0.023 17MOL O 17 -0.248 -0.031 0.103 18MOL N 18 -0.342 0.012 0.194 19MOL C 19 -0.429 -0.070 0.271 20MOL O 20 -0.449 -0.192 0.246 21MOL C 21 -0.487 0.001 0.389 22MOL C 22 -0.418 0.139 0.387 23MOL C 23 -0.331 0.133 0.266 24MOL O 24 -0.254 0.226 0.231 10.00000 10.00000 10.00000

coarse_grained.gro

MOL generated from auto_martini.py 8 1MOL S01 1 -0.089 -0.082 -0.155 2MOL S02 2 -0.070 -0.269 0.022 3MOL S03 3 0.140 -0.149 -0.061 4MOL S04 4 0.444 -0.079 -0.160 5MOL S05 5 0.342 0.111 -0.216 6MOL P01 6 -0.248 -0.031 0.103 7MOL S06 7 -0.429 -0.070 0.271 8MOL S07 8 -0.331 0.133 0.266 10.00000 10.00000 10.00000

glosar commented 9 years ago

Dear Tristan,

thank you very much,

Gloria

tbereau / auto_martini

Assertion `!posix::pthread_mutex_destroy(&m)' failed. #1

mol.itp

atomistic.gro

coarse_grained.gro