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How to visualize rotatable groups after a Glide job

1/3/2013

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Before docking with Glide and during receptor Grid generation, you have the possibility to select which hydroxyl and thiol groups around your ligand will be rotating in order to form hydrogen bonds.

After performing Glide docking you have to save your project file so that for each ligand the correct Ser/Thr/Cys rotamer is displayed in the pose viewer file. In order to include this information in your saved files, you have to follow this procedure:

1) Import the *_pv.maegz with your top-scored compounds in Maestro


2) In another Maestro window import the *.sdf file containing the exemplar compounds of each of the initial clusters.

3) In the Project Table of the first Maestro window, select (Control and right mouse click on the entry) AND include (Control and right mouse click on the box of the table entry so that it turns from empty full (black): the displayed atoms (i.e. the protein) plus each of the exemplar compounds that we see in the second Maestro window.

4) Export the selected/included entries into a *maegz file that MUST end with "_pv", e.g. "exemp1_pv.maegz", making also sure that the option "All properties" in the Export pop-up window is selected.

George


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Visualize Glide XP scoring function terms with XP Visualizer

12/10/2012

1 Comment

 
Glide XP Visualizer, visualizes Glide XP scoring function terms in Maestro. Its main  functions are:
  • To display the Glide XP results from a pose viewer file (jobname_pv.mae) in a table of XP terms for each ligand.
  • To provide 3D visualizations for XP terms. Information for these visualizations is read from the pose viewer file. The descriptor file (jobname.xpdes), which is also generated by Glide XP, can be used instead; it must be in the same directory as the pose viewer file.
  • To allow selective evaluation of ligands (and groups of ligands) within the table. This helps you analyze ligands separately during the screening process.
Before you can use the Glide XP Visualizer, you must generate the descriptor information. This information is not included in a normal XP run. To generate it, select Write XP descriptor information in the Settings tab of the Ligand Docking panel. You should also select Write pose viewer file in the Output tab of the Ligand Docking panel to write the required pose viewer file.

If you forgot to check the 'Write XP descriptor information' option and have results of a long XP job and don't want to rerun it in order to generate the descriptors, you could run an XP job on your previous results with the "Ligand sampling" option set to "None (score in place only)". This will re-score the ligands (and add XP descriptors if you've selected that option), which is much faster than re-docking the ligands.

Eva


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How to restart a Glide job that crashed

10/31/2012

2 Comments

 
While running, Glide saves the output in a temporary directory. The location of the temporary directory is found in the .file that is being stored in the directory from where you launched the job. Usually it is in /scratch.
In the temporary directory you should locate and save the _raw.maegz file which contains the Glide results up to the point when your job crashed. Then, open the .log file and see what is the ligand number when your job stopped. Rename the .in file and open it. Change the LIGAND_START parameter to the ligand number that you experienced the crash.

Another way to recover the job is to list the active (and unfinished) jobs with "jobcontrol".
As mentioned in the jobcontrol manual you can type
"$SCHRODINGER/jobcontrol -list" to list all the active jobs and
"$SCHRODINGER/jobcontrol -recover <jobid>" to recover your job, which means that the _raw.maegz file will be simply copied in the original working directory.

The last option, which I have not tried is to restart the Glide job with the
"$SCHRODINGER/glide -restart" option, which however works only for distributed glide jobs (as mentioned in the manual).

Zoe

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How to run Glide faster on a desktop

7/31/2012

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We recently realized that using the "-LOCAL" flag in the /opt/schrodinger/glide command, the program will write to the current working directory resulting in a speed up of ~20%.

The command you should use is:

/opt/schrodinger/glide -LOCAL file.in


Evi
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