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Virtual Screening Workflow with the ZINC library on the apple cluster

3/6/2014

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SP
Make a directory and include the following files:
  • make_dirs
  • copy_files2
  • glide-dock_SP_0.in
Example of SP.in file:
USECOMPMAE YES
NREPORT 30000
RINGCONFCUT 2.500000
GRIDFILE /home/eva/Zinc_screening/SP_1MV9/1MV9_no_wat_glide-grid.zip
LIGANDFILE /home/ZINC/druglike-Zinc-library-mol2/3_p0.0.mol2
LIGFORMAT mol2
  1. Run the make_dirs script --> creates 88 folders (0-87)
  2. Run the copy_files2 script --> leave the glide-dock_SP_0.in file out of its folder to run the script and when it is finished then cut+paste it to folder_0.
  3. Use the submit_SP_all script to run the SP on apple cluster. In my case I used to put up to 12 jobs in each node ( modify this line of the script: for (( i = 76 ; i<=87; i++   )) ). Due to the fact that the jobs were put randomly to the nodes and in order to have up to 12 jobs on each node, I was using first some "fake" gromacs runs to use 12 cores and left the other 12 free for screening runs (Evi's idea! Thank's Evi!!).
  4. When the run is finished you should check all the 88 directories and see if you have outputs like: e.g. glide-dock_SP_8_pv.maegz. If something goes wrong and the run has stopped then you will see e.g. glide-dock_SP_8_raw.maegz as an output. Then you should copy your glide-dock_SP_8.in to glide-dock_SP_8_b.in and run it from the ligand that it had stopped. Finally, you will have: glide-dock_SP_8_raw.maegz and glide-dock_SP_8_b_pv.maegz. Both are useful! Don't delete the first one!
  5. In order to finish the SP process you have to take the top-scored 40.000 compounds from all the directories and put them to a new file (SP_top40000_1MV9_pv.maegz) to use as an input for the XP process.
You can run the GlideSortScript_ZINC.csh script to acheive this result. The content of the script is the following: (You have to add the possible raw.maegz files,too.)
/opt/schrodinger/utilities/glide_sort -n 40000 -o SP_top40000_1MV9_pv.maegz -r  SP_top40000_1MV9.rept -hbond_cut 0.00 -cvdw_cut 0.00 -metal_cut 10.00 \ db3_p0.0/glide-dock_SP_0_pv.maegz \db3_p0.1/glide-dock_SP_1_pv.maegz \db3_p0.2/glide-dock_SP_2_pv.maegz \db3_p0.3/glide-dock_SP_3_raw.maegz \db3_p0.3/glide-dock_SP_3_b_pv.maegz \ etc.


XP
Each XP directory includes:
  • grid.zip file
  • SP_top40000_1MV9_pv.maegz (output of SP)
  • XP.in files (I split them into 8 files in my case) 

Example of XP.in file:
WRITEREPT YES
WRITE_RES_INTERACTION YES
WRITE_XP_DESC YES
USECOMPMAE YES
POSTDOCK_NPOSE 10
LIGAND_END 10000
LIGAND_START 5001 (this line is not included in the XP_1.in file as it starts from the beginning)
MAXREF 800RINGCONFCUT 2.500000
GRIDFILE /home/eva/XP_Zinc/1MV9_XP_Zinc_2_8/1MV9_no_wat_glide-grid.zip
LIGANDFILE /home/eva/XP_Zinc/1MV9_XP_Zinc_2_8/SP_top40000_1MV9_pv.maegz
PRECISION XP


So, I split it to 8 XP directories:
0 - 5000, 5001  - 10000, 10001 - 15000, ..., 35001 - 40000


Run each one on the cluster or on our PCs manually :
/opt/schrodinger/glide 1MVC_Zinc_XP1.in -HOST xgrid-server
/opt/schrodinger/glide 1MVC_Zinc_XP2.in -HOST xgrid-server etc. 

Finally you take the top-scored 1000 compounds (as we did before for the SP process where we took the 40.000 top-scored ) using the same script (GlideSortScript_ZINC.csh):

/opt/schrodinger2012/utilities/glide_sort -n 1000 -o  file_XP_1000_pv.maegz -r  file_XP_1000_.rept -hbond_cut 0.00 -cvdw_cut 0.00 -metal_cut 10.00 glide-dock_XP_0_pv.maegz glide-dock_XP_1_pv.maegz glide-dock_XP_2_pv.maegz glide-dock_XP_3_pv.maegz glide-dock_XP_4_pv.maegz glide-dock_XP_5_pv.maegz glide-dock_XP_6_pv.maegz glide-dock_XP_7_pv.maegz glide-dock_XP_8_pv.maegz

Some useful tips:

Run faster with the -LOCAL flag:
/opt/schrodinger/glide -LOCAL file.in

path for ZINC on apple:
/Network/Servers/xgrid-Server.xgrid/Volumes/RAID/NetUsers/pgkeka/PI3K/Screening/ZINC/druglike-Zinc-library-mol2/

Apple cluster run-command:
/opt/schrodinger/glide your_XP_file.in -HOST xgrid-server
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Peptide docking with Glide

10/3/2013

1 Comment

 
In this article, Senior Application Scientist Thijs Beuming discusses the development of a new Glide docking protocol designed specifically for peptides.
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How to setup passwordless ssh access between nodes in a cluster

5/8/2013

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To run the Schrodinger Suite on the cluster as well as many other programs, you require passwordless ssh.

To use passwordless ssh, the hosts to which you want to connect must be configured to satisfy the following requirements:

• Ansshd server must be running.
• RSA public key authentication must be enabled and empty passphrases must be allowed
in the sshd configuration.
Note: Public key authentication is enabled in OpenSSH by default.

The following steps allow you to use ssh between computers that share your login directory
without specifying a password.

1. Generate a public/private RSA key pair on a host of your choice, whose home directory is
shared with the remote hosts that you want to run jobs on:
cd ~/.ssh
ssh-keygen -t rsa
Note: When asked for a passphrase do not enter one; just press ENTER. If you specify a
passphrase it defeats the purpose of configuring passwordless ssh.
2. Add your public key to the list of keys allowed to log in to your account:
cat id_rsa.pub >> authorized_keys
cat id_rsa.pub >> authorized_keys2
The two separate files are necessary to support both OpenSSH 1.5 and OpenSSH 2.0 protocols.
Some versions use just one or the other of these files.
3. Suppress the confirmation dialog you ordinarily get when you connect to a machine for
the first time:
echo "StrictHostKeyChecking no" >> config
This is necessary if you want to use ssh non-interactively and you cannot get RSA signatures
for every host to which you want to allow connections in your known_hosts file
ahead of time.
4. Remove your known_hosts file:
rm known_hosts*
This is necessary so that the new RSA key-pair mechanism is used for every host. Otherwise,
hosts to which you previously connected using passwords might not use the new
system automatically.
5. Make sure your home directory cannot be written by anyone but you:
chmod go-w ~
This is required before ssh will allow passwordless access to your account.
For each home directory that is not shared with that of the chosen host:
1. Copy the public and private keys to that home directory:
scp ~/.ssh/id_rsa* other-host/~/.ssh/
2. Connect to the host on which that home directory is mounted and change to the .ssh
directory:
cd ~/.ssh
3. Repeat Step 2 through Step 5 above.
4. Ensure that id_rsa (the private key) is readable and writeable only by the user:
chmod go-rwx ~/.ssh/id_rsa

Taken from the Job Control Guide of the Schrodinger Suite

Zoe

2 Comments

Schrodinger Suite problem

5/8/2013

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If you see the following error from the Schrodinger Suite:

root@hauptman:~# $SCHRODINGER/licadmin SERVERUP -c $SCHRODINGER/license
-l lmgrd.`hostname`.log
License file: /home/minghan/schrodinger2012//license (commandline)
Log file: lmgrd.hauptman.log
/home/minghan/schrodinger2012//licadmin: 1: eval:
/home/minghan/schrodinger2012/mmshare-v21025/bin/Linux-x86_64/lmgrd: not found

it usually means that the lsb libraries are not installed on the machine. Please see the following Knowledge Base article:

http://www.schrodinger.com/kb/1437

for instructions for installing these libraries. The lsb libraries are required for running the lmgrd and SCHROD processes so may not be necessary for the node-locked license. However, if you cannot run Maestro, installing the lsb libraries may be a good start.

Zoe


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Visualize an trajectory created by Impact (Schrodinger)

3/11/2013

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To visualize an impact trajectory, open the panel with the Impact parameters before starting the run and click on "Record Trajectory", which is deselected by default. The option is under: Applications -> Impact -> Dynamics -> MD Parameters -> Record Trajectory".
After your trajectory is ready, you will see a "T" in your project table. Click on the "T" and a trajcetory viewing panel will open.

To prepare a video file for incorporation into PowerPoint showing your modelling results you can use the following options:
  • You can create a movie in MPEG format of the selected entries in the Project Table with Entry → Record Movie.
  • From Suite 2010 on you can create a movie in MPEG format of a sequence of Workspace views, by clicking Record Movie in the Manage Views panel.
  • You can record a movie of a Desmond (or Impact) trajectory, in the Trajectory panel.
  • You can use the Maestro Viewer ActiveX control in a PowerPoint presentation, to show a structure in a Maestro window, and manipulate it (rotate, translate, zoom) in the presentation.
See also:


http://www.schrodinger.com/kb/354

Zoe


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Schrodinger's March 2013 webinars: Phase Shape, ensemble docking, and materials applications

2/27/2013

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Schrodinger's March 2013 seminar series begin next Tuesday, March 5. This seminar series will include presentations on Phase Shape for ligand-based shape screening and new ensemble docking practices to account for protein flexibility.

Schrodinger is also debuting a Materials Science Suite this year - Dr. Vyacheslav S. Bryantsev of Liox Power will also be presenting on computational modeling of rechargeable Li-air battery materials on March 7. Please feel free to invite your colleagues in the materials industries to join us for this materials-focused presentation!

Here is the full webinar list with dates:

Accounting for protein flexibility in virtual screening using ensemble docking

Dr. Woody Sherman
Schrödinger's Vice President, Applications Science
Abstract March 5, 2013
10 am ET Register
1pm ET Register

Computational Modeling of Rechargeable Li-Air Battery Materials
Dr. Vyacheslav S. Bryantsev
Liox Power, Senior Scientist
Abstract March 7, 2013
10 am ET Register

Using Phase Shape for rapid ligand alignment and virtual screening
Dr. Woody Sherman
Schrödinger's Vice President, Applications Science
Abstract March 12, 2013
10 am ET Register
1pm ET Register
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How to visualize rotatable groups after a Glide job

1/3/2013

0 Comments

 
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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Comparing Binding Sites with SiteMap

12/12/2012

0 Comments

 
When looking for diversity in protein structures, the volume-based or the shape-based analysis of a binding side through SiteMap is more meaningful  than looking at the RMSD metric alone, as mentioned in a recent protein preparation Schrodinger webinar by Dr Woody Sherman, which can be found here:
http://www.schrodinger.com/seminarprior/19/38/

To evaluate protein structure diversity with SiteMap you can perform the following steps:
1. Run SiteMap on each structure -- Computes shape of binding pocket for each structure
3.Generate pairwise volume overlap matrix with the Python script from Script Center "trajectory_binding_site_volumes.py"
4.Perform hierarchical clustering to get diverse binding sites with "volume_cluster.py"
5. Choose desired structures


See also:
Halgren T (2007) Chem Biol Drug Des 69(2):146 title: "New method for fast and accurate binding-site identification and analysis."

Halgren T (2009) J Chem Inf Model 49:377 title: "Identifying and characterizing binding sites and assessing druggability."

Eva


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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


1 Comment

Contact Module in Maestro - contact cutoff ratio

11/30/2012

1 Comment

 
In Maestro when visualizing a structure file, you can  select Tools -> Measurements -> Contacts panel in order to see Good contacts and Bad&Ugly contacts. When contacts are displayed, good contacts are green by default, bad ones are orange, and ugly ones are red. These criteria whether a contact is defined as good, bad or ugly are based on the following formula:

C = D12 / ( R1 + R2 )

where D12 is the distance between atomic centers 1 and 2, and R1 and R2 are the radii of atomic centers 1 and 2. C is defined as the "contact cutoff ratio" in Maestro and has default values of 0.85 for "Bad" contacts and 0.70 for "Ugly" contacts. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). These three values then provide 4 ranges. Distances greater than C(good) are not marked, less than C(good) but greater than C(bad) are marked as "good", etc.

This answer was provided by the Schrodinger help team.

Zoe

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