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
screen3d not converging
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
Aiden

Joined: 11 Oct 2013
Posts: 17

View user's profile

Back to top
Link to postPosted: Tue Aug 19, 2014 4:41 amPost subject: screen3d not converging Reply with quote

Hello,

I have recently started using screen3d to preform structure comparisons, and have been getting the message:

Aug 18, 2014 8:27:45 PM chemaxon.marvin.alignment.AlignmentBase optimization

INFO: Optimization was not converged.

How can I avoid this? It is only happening for about half the structures I am screening, but it has me stumped! can I increase the time allowed, or would this help?

I am using screen3d as follows:

screen3d s -t ncidiv.ser -q Abacavir.ser frq 

Where ncidiv.ser is a list of ~1600 structures. Would it be possible to view which structure is throwing the errors so that it may be examined or removed?

 

OS: 64 bit linux

JChem 14.8.4.0

Thank you in advance! Your tools have been indispensable. 

Aiden

Joined: 11 Oct 2013
Posts: 17

View user's profile

Back to top
Link to postPosted: Tue Aug 19, 2014 5:31 amPost subject: also Reply with quote

is there any significant difference from the Alignment package included in marvin beans? I am trying to do rigid-rigid alignment.

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

View user's profile

Back to top
Link to postPosted: Tue Aug 19, 2014 12:34 pmPost subject: Reply with quote

Hi ajaceves,

the problem you encountered is due to the internal optimizer in the alignment module. This means that some

optimization runs do not meet the convergence criteria. In this case that info message is given, and the run

continues. This issue does not influence the similarity result for a query-target pair. 

The alignment module is also built in MarvinSketch as a plugin (3D Flexible Alignment Plugin), but that is only able

to superimpose 1 ensemble (or pair) of molecules.

 

Best regards,

Daniel 

Aiden

Joined: 11 Oct 2013
Posts: 17

View user's profile

Back to top
Link to postPosted: Tue Aug 19, 2014 4:50 pmPost subject: Reply with quote

Hello Daniel,

Thank you for your prompt and informative reply! 

If I may ask one other question... Is the default method rigid-flexible? I am aware of the switch for force the query to be rigid, but how does one control the rigid/flex state of the target? Thank you again for your support.

Aiden

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

View user's profile

Back to top
Link to postPosted: Wed Aug 27, 2014 4:03 pmPost subject: Reply with quote

Hi Aiden, 

yes, there is an option for this. So to keep the target rigid, omit the -F option that forces the target to be flexible during the first phase of the screening. This is the default, by the way. So for example

screen3d g ada_ligands.mol2 -match

uses the Match screening method, but keeps the target molecules in the file rigid during the preparation phase.

In the Alignment Plugin you just have to select the molecule on the canvas that you want to treat rigid.

You can reach the manual of the screen3d tool by typing

screen3d -h 

I hope this helps.

Daniel

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