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

from auto_martini.

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

from auto_martini.

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

from auto_martini.

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 [email protected]
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:
#1 (comment)

from auto_martini.

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 [email protected] 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 [email protected]
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:
#1 (comment)

—
Reply to this email directly or view it on GitHub
#1 (comment).

from auto_martini.

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 [email protected]
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
[email protected] 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 [email protected]
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:

#1 (comment)

—
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GitHub
#1 (comment).

---

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GitHub:
#1 (comment)

from auto_martini.

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 [email protected] 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 [email protected]
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
[email protected] 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 [email protected]
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:

#1 (comment)

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

---

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GitHub:
#1 (comment)

—
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#1 (comment).

from auto_martini.

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 [email protected]
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
[email protected] 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 [email protected]
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
[email protected] 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 [email protected]
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:

#1 (comment)

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

---

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GitHub:

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GitHub
#1 (comment).

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from auto_martini.

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

from auto_martini.

Dear Tristan,

thank you very much,

Gloria

from auto_martini.