Technical Support Forum Index
Technical Support Forum
Access ChemAxon scientists and developers here. For registration and login issues contact website support.

Support Ticket System is replacing forum

This forum was converted into a searchable archive. You cannot add posts here any more. For support please use our new Ticket System.

Create your first ticket
LogP of isomers
To watch this topic for replies  Register (enables digests) or give email address:
This topic is locked: you cannot edit posts or make replies.
Display posts from previous:   
    View previous topic :: View next topic    
Author Message
TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Thu Apr 02, 2009 9:56 amPost subject: LogP of isomers Reply with quote

I have two isomers and the calculation of Logp give me 2 different results?

Why? In the last version of MarvinBeans (4), the 2 LogP are the same.
Jozsef
ChemAxon personnel
Joined: 25 May 2004
Posts: 568

View user's profile

Back to top
Link to postPosted: Fri Apr 03, 2009 2:46 pmPost subject: Reply with quote

Hi,


"Isomer1" and "isomer2" are  tautomers of each others.  Since their structures are different this is why their calculated logP (based on molecular topology) will be different as well.


Identical logP value will be calculated if you switch on the "Take major tautomeric form"  option.


(Please note that your attached files "isomer1" and "isomer2" are identicals.)


Jozsi
TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Fri Apr 03, 2009 3:08 pmPost subject: Reply with quote

sorry i correct isomer2.mol
Jozsef
ChemAxon personnel
Joined: 25 May 2004
Posts: 568

View user's profile

Back to top
Link to postPosted: Fri Apr 03, 2009 3:58 pmPost subject: Reply with quote

Hi,

Ok, thanks.

Jozsi
TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Mon Apr 06, 2009 9:58 amPost subject: Reply with quote

Normally, I calculate Logp with :

 

cxcal -N hi test.sdf logp -p 3

 

I try to add the option M  but it doesn't work.

If I try only :

cxcalc logp -M isomer1.mol

it works but I would like to remove the id

 

cxcalc logp -M N hi isomer1.mol => doesn't work

TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Mon Apr 06, 2009 10:00 amPost subject: Reply with quote

Ok I find :cxcalc -N hi logp logP -M isomer1.mol -p 3

 

 

TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Mon Apr 06, 2009 10:01 amPost subject: Reply with quote

correction : cxcalc -N hi logp -M isomer1.mol -p 3

TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Wed Apr 15, 2009 10:15 amPost subject: Reply with quote

cxcalc -N hi logp -M isomer1.mol -p 3 is correct?

or cxcalc -N hi logp -M true isomer1.mol -p 3 is correct?

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

View user's profile

Back to top
Link to postPosted: Wed Apr 15, 2009 10:27 amPost subject: Reply with quote

Both are correct. In case of [true|false] parameters true can be omitted.

Zsolt

TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Wed Apr 15, 2009 2:10 pmPost subject: Reply with quote

I have problem with the structure joined.

cxcalc -N hi logp -M 2008-10-30_6_L.mol -p 3 => the time of calculation is too long

 

If i remove the "-M", the time of calculation is normal

TRAN-MINH

Joined: 13 Oct 2005
Posts: 277

View user's profile

Back to top
Link to postPosted: Thu Apr 16, 2009 1:44 pmPost subject: Reply with quote

No idea?

So I remove the option M of my calculation of logP

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

View user's profile

Back to top
Link to postPosted: Fri Apr 17, 2009 11:19 amPost subject: Reply with quote

It is a quite large molecule, and calculating the major tautomer of a large molecule takes time. Without the tautomer calculation (-M option) it is much more faster.

Anyway, it seems the tautomer calculation in this case is really slow, so we will check it.

This topic is locked: you cannot edit posts or make replies.
Page 1 of 1


To watch this topic for replies   Register (enables digests) or give email address  
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You cannot download files in this forum