I intensively docked the receptor by the ligand repeating any times to received multidocked rec-n*lig system. From any docking step i have received the response the same as starting previous step without addition of new ligand. I have seen output files and marked that unsuccessful docking folders haven't the file with .rept, for example iggdocked.rept. Why this file is lost and how to prevent this unhappy in next docking studies?
Hi Roman Boroznjak, Thanks for your comment. There might be a few different reasons why the files are getting lost, but it is hard to say without a little bit more information. Could you please email us at help@schrodinger.com and attach any files you have from the failed docking job? Best regards, Jarred
WARNING Constraint "position1" has no SMARTS patterns defined. You must define at least one pattern for this constraint before this job can be written or started. To define patterns for this constraint, select it in the Constraints folder, and click Edit Feature.
krunal patel Unlike H-bond and metal constraints, where reasonable default ligand features are known that can satisfy the constraints, a positional constraint is a very generic type of constraint. Therefore, it is necessary for the user to define (via a set of SMARTS patterns) the ligand features that can satisfy the constraint. Please see Section of 3.9 of the Glide Quick Start Guide for a tutorial on using a positional constraint. Sorry, I don't think we have a tutorial video for this yet. If you have further questions, please submit queries via email or our web form... www.schrodinger.com/supportcenter/ Sincerely, Jeff Saunders Schrodinger Technical Support
Sir, After 2 successful docking with the ligand, I forgot all the steps. Actually the sequence of tabs that will be hited. Please help to elaborate the tab sequences i.e. 1. Task > PDB id > prepn wizard>preprocess> refinement> minimize 2.????? please help stating the tabs sequentially
I'm not understanding what the purpose of this gridding is. Why couldn't this just be as simple as MOE you find a site you want to dock to and voila its done. How the hell would I know what spheres to make what size and what spheres to put up my ass which ones to put on a nitrogen??
![[OUTDATED] Receptor Grid Generation (All)](http://i.ytimg.com/vi/_AUKLGtrBR8/mqdefault.jpg)
![[OUTDATED] Receptor Grid Generation (All)](/img/tr.png)
![[OUTDATED] Ligand Preparation with LigPrep](http://i.ytimg.com/vi/5vO88ui0JdM/mqdefault.jpg)
Please see updated information at learn.schrodinger.com/private/edu/release/current/Documentation/html/glide/glide_home.htm?
Thank you for this video.
Do you have a serie on the post docking processing ?
What is the command line equivalent of what you just did?
I intensively docked the receptor by the ligand repeating any times to received multidocked rec-n*lig system. From any docking step i have received the response the same as starting previous step without addition of new ligand. I have seen output files and marked that unsuccessful docking folders haven't the file with .rept, for example iggdocked.rept.
Why this file is lost and how to prevent this unhappy in next docking studies?
Hi Roman Boroznjak,
Thanks for your comment. There might be a few different reasons why the files are getting lost, but it is hard to say without a little bit more information. Could you please email us at help@schrodinger.com and attach any files you have from the failed docking job?
Best regards,
Jarred
i want to apply constrain in docking. but getting error in glide ligad run. any tutorial video available?
WARNING Constraint "position1" has no SMARTS patterns defined. You must define at least one pattern for this constraint before this job can be written or started. To define patterns for this constraint, select it in the Constraints folder, and click Edit Feature.
krunal patel Unlike H-bond and metal constraints, where reasonable default ligand features are known that can satisfy the constraints, a positional constraint is a very generic type of constraint. Therefore, it is necessary for the user to define (via a set of SMARTS patterns) the ligand features that can satisfy the constraint. Please see Section of 3.9 of the Glide Quick Start Guide for a tutorial on using a positional constraint. Sorry, I don't think we have a tutorial video for this yet.
If you have further questions, please submit queries via email or our web form...
www.schrodinger.com/supportcenter/
Sincerely,
Jeff Saunders
Schrodinger Technical Support
ok thank you for your response.
What are the specs to run this software?
Sir, After 2 successful docking with the ligand, I forgot all the steps. Actually the sequence of tabs that will be hited. Please help to elaborate the tab sequences i.e.
1. Task > PDB id > prepn wizard>preprocess> refinement> minimize
2.?????
please help stating the tabs sequentially
I'm not understanding what the purpose of this gridding is. Why couldn't this just be as simple as MOE you find a site you want to dock to and voila its done. How the hell would I know what spheres to make what size and what spheres to put up my ass which ones to put on a nitrogen??