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Command line help for protonation

Stuart
Dear OpenBabel community,

I am a new user and would like to use OpenBabel in order to perform the following tasks on a small molecule (let's say the starting point is a molecule represented as a smiles string). I'm having some difficulty with the third step and would really appreciate some help from you veteran Bablers out there.

1. Convert molecule from smiles to sdf format, with generation of 3D co-ordinates. I can do this with the following command:

obabel infile.smi -O outfile.sdf --gen3D

2. Remove all the hydrogens created during sdf generation:

obabel outfile.sdf -O outfile_noH.sdf -d

3. Add hydrogens only present at pH 7.4:

obabel outfile_noH.sdf -O outfile_H.sdf -p 7.4

When I enter the command above, nothing happens in the terminal and it just keeps running...and running. Eventually, I just cancel the operation because nothing is done (well, a junk 28 k file is written that is not a real sdf). Am I entering the wrong syntax or somthing? I've even tried the above command minus the 7.4, but it still doesn't work. If someone can help with this command for the third step that would be great.

Thanks.

Stuart
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Re: Command line help for protonation

Pascal Muller-3
Hi,




I am a new user and would like to use OpenBabel in order to perform the
following tasks on a small molecule (let's say the starting point is a
molecule represented as a smiles string). I'm having some difficulty with
the third step and would really appreciate some help from you veteran
Bablers out there.

1. Convert molecule from smiles to sdf format, with generation of 3D
co-ordinates. I can do this with the following command:

obabel infile.smi -O outfile.sdf --gen3D

2. Remove all the hydrogens created during sdf generation:

obabel outfile.sdf -O outfile_noH.sdf -d

3. Add hydrogens only present at pH 7.4:

obabel outfile_noH.sdf -O outfile_H.sdf -p 7.4


When I enter the command above, nothing happens in the terminal and it just
keeps running

These commands are working fine for me, starting with CCC(=O)O.
Does this smiles fail for you too?
What's your input smiles?

Regards,
Pascal


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Re: Command line help for protonation

mirix
In reply to this post by Stuart
Hi Stuart,

I have you tried removing the space between the "-p" flag and the value, like "-p7.4"?

Best,

Miro


--
Edelmiro Moman, PhD
Department of Molecular Medicine
Royal College of Surgeons in Ireland

POSTAL ADDRESS:

L5.08
Trinity Biomedical Sciences Institute - TBSI
Trinity College Dublin
152 - 160 Pearse St
Dublin 2
IRELAND

Phone: +353 (0)1 896 3527

On 4 August 2016 at 22:00, Stuart <[hidden email]> wrote:
Dear OpenBabel community,

I am a new user and would like to use OpenBabel in order to perform the
following tasks on a small molecule (let's say the starting point is a
molecule represented as a smiles string). I'm having some difficulty with
the third step and would really appreciate some help from you veteran
Bablers out there.

1. Convert molecule from smiles to sdf format, with generation of 3D
co-ordinates. I can do this with the following command:

obabel infile.smi -O outfile.sdf --gen3D

2. Remove all the hydrogens created during sdf generation:

obabel outfile.sdf -O outfile_noH.sdf -d

3. Add hydrogens only present at pH 7.4:

obabel outfile_noH.sdf -O outfile_H.sdf -p 7.4

When I enter the command above, nothing happens in the terminal and it just
keeps running...and running. Eventually, I just cancel the operation because
nothing is done (well, a junk 28 k file is written that is not a real sdf).
Am I entering the wrong syntax or somthing? I've even tried the above
command minus the 7.4, but it still doesn't work. If someone can help with
this command for the third step that would be great.

Thanks.

Stuart



--
View this message in context: http://forums.openbabel.org/Command-line-help-for-protonation-tp4659417.html
Sent from the General discussion mailing list archive at Nabble.com.

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Re: Command line help for protonation

Stuart
In reply to this post by Pascal Muller-3

Dear Pascal,

 

Thanks you for your help. Steps 1 and 2 work fine (i.e. conversion of smiles to 3D-sdf, then removal of hydrogens), but step 3 still does not work. The smiles of the small molecule I am using is ‘CC1=C(SC2=C1C(=N[C@H](C3=NN=C(N32)C)CC(=O)OC(C)(C)C)C4=CC=C(C=C4)Cl)C’

 

Can you or anyone else think of what the problem may be?

 

Stuart

 

 

From: Pascal Muller [mailto:[hidden email]]
Sent: Friday, August 05, 2016 4:21 AM
To: Stuart Ember
Cc: babel
Subject: Re: [Open Babel] Command line help for protonation

 

Hi,

 

 


I am a new user and would like to use OpenBabel in order to perform the
following tasks on a small molecule (let's say the starting point is a
molecule represented as a smiles string). I'm having some difficulty with
the third step and would really appreciate some help from you veteran
Bablers out there.

1. Convert molecule from smiles to sdf format, with generation of 3D
co-ordinates. I can do this with the following command:

obabel infile.smi -O outfile.sdf --gen3D

2. Remove all the hydrogens created during sdf generation:

obabel outfile.sdf -O outfile_noH.sdf -d

3. Add hydrogens only present at pH 7.4:

obabel outfile_noH.sdf -O outfile_H.sdf -p 7.4

 


When I enter the command above, nothing happens in the terminal and it just
keeps running

 

These commands are working fine for me, starting with CCC(=O)O.

Does this smiles fail for you too?

What's your input smiles?

Regards,

Pascal

 


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Re: Command line help for protonation

Stuart
In reply to this post by mirix

Dear Miro,

 

Thanks for your help and suggestion. However, removing the space between –p and 7.4 (i.e. –p7.4) changes the syntax such that –p is no longer recognized as a real option parameter, and the command does not run.

 

The small molecule smiles I am using is ’CC1=C(SC2=C1C(=N[C@H](C3=NN=C(N32)C)CC(=O)OC(C)(C)C)C4=CC=C(C=C4)Cl)C’

 

Do you have any other suggestions or can anyone else comment on the problem?

 

Stuart

 

 

From: Miro Moman [mailto:[hidden email]]
Sent: Friday, August 05, 2016 4:29 AM
To: Stuart Ember
Cc: [hidden email]
Subject: Re: [Open Babel] Command line help for protonation

 

Hi Stuart,

I have you tried removing the space between the "-p" flag and the value, like "-p7.4"?

Best,

Miro


--
Edelmiro Moman, PhD
Department of Molecular Medicine
Royal College of Surgeons in Ireland

POSTAL ADDRESS:

L5.08
Trinity Biomedical Sciences Institute - TBSI
Trinity College Dublin
152 - 160 Pearse St
Dublin 2
IRELAND

Phone: +353 (0)1 896 3527

 

On 4 August 2016 at 22:00, Stuart <[hidden email]> wrote:

Dear OpenBabel community,

I am a new user and would like to use OpenBabel in order to perform the
following tasks on a small molecule (let's say the starting point is a
molecule represented as a smiles string). I'm having some difficulty with
the third step and would really appreciate some help from you veteran
Bablers out there.

1. Convert molecule from smiles to sdf format, with generation of 3D
co-ordinates. I can do this with the following command:

obabel infile.smi -O outfile.sdf --gen3D

2. Remove all the hydrogens created during sdf generation:

obabel outfile.sdf -O outfile_noH.sdf -d

3. Add hydrogens only present at pH 7.4:

obabel outfile_noH.sdf -O outfile_H.sdf -p 7.4

When I enter the command above, nothing happens in the terminal and it just
keeps running...and running. Eventually, I just cancel the operation because
nothing is done (well, a junk 28 k file is written that is not a real sdf).
Am I entering the wrong syntax or somthing? I've even tried the above
command minus the 7.4, but it still doesn't work. If someone can help with
this command for the third step that would be great.

Thanks.

Stuart



--
View this message in context: http://forums.openbabel.org/Command-line-help-for-protonation-tp4659417.html
Sent from the General discussion mailing list archive at Nabble.com.

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Re: Command line help for protonation

Geoff Hutchison
In reply to this post by Stuart
Can you or anyone else think of what the problem may be?

No. It would certainly help if you gave more information on what platform (OS) you're using and the version of Open Babel.

-Geoff


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Re: Command line help for protonation

Stuart

Hi Geoff,

 

I’m using Open Babel 2.3.2. on a Windows 10 system.

 

Stuart

 

From: Geoffrey Hutchison [mailto:[hidden email]]
Sent: Friday, August 05, 2016 12:40 PM
To: Stuart Ember
Cc: Pascal Muller; babel
Subject: Re: [Open Babel] Command line help for protonation

 

Can you or anyone else think of what the problem may be?

 

No. It would certainly help if you gave more information on what platform (OS) you're using and the version of Open Babel.

 

-Geoff

 


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Re: Command line help for protonation

Pascal Muller-3
Hi,

Starting with your smiles, converting "outfile_noH.sdf" to "outfile_H.sdf" with the -p 7.4 option (or an other value) doesn't work for me either. It keeps running, like you said (Open Babel 2.3.2, Linux Ubuntu 14.04).

But with this compound with a double bond changed to a single bond, it works:
CC1=C(C)C2=C(S1)N1C(NN=C1C)[C@H](CC(=O)OC(C)(C)C)N=C2C1=CC=C(Cl)C=C1

So I guess the unusual nitrogens cycle is involved somehow.

Anyway, the compound should not be protonated at pH 7.4... :)

Regards,
Pascal


2016-08-05 19:28 GMT+02:00 Stuart Ember <[hidden email]>:

Hi Geoff,

 

I’m using Open Babel 2.3.2. on a Windows 10 system.

 

Stuart

 

From: Geoffrey Hutchison [mailto:[hidden email]]
Sent: Friday, August 05, 2016 12:40 PM
To: Stuart Ember
Cc: Pascal Muller; babel
Subject: Re: [Open Babel] Command line help for protonation

 

Can you or anyone else think of what the problem may be?

 

No. It would certainly help if you gave more information on what platform (OS) you're using and the version of Open Babel.

 

-Geoff

 



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