In some cases, when installing Desmond software, the following error message can appear:

556: Illegal number: unknownunknown

You can use the following procedure to replace the original platform file with the updated one. You must have write permissions to your SCHRODINGER directory to perform this update.

1. Back up the original platform file:
   
   mv $SCHRODINGER/platform $SCHRODINGER/platform.orig
   
2. Right-click on the following link and choose to save it as a file (Save Link As):
   
   ftp://ftp.schrodinger.com/support/hidden/TS/platform_118130
   
   You should save it to your SCHRODINGER (installation) directory with the name platform. If you have a problem saving the file, then save it to another directory and move it to $SCHRODINGER/platform.

Now that the platform file has been replaced in your SCHRODINGER installation directory, try to start Maesto or run machid once again.

(source: http://www.schrodinger.com/kb/1528)

Harris

All of these tips are excellent and absolutely needed for mastering presentations. Some of the tips are adapted from this article.

1. Do You have a Special Message to Deliver?
Remember that you are giving this talk because you have a special message to deliver to the audience. You should determine the specifics that you want to get across. What does your audience want to hear and can you deliver that kind of message? Being too general or vague will simply minimize your chances of success before you have even gotten started. Work through that message and try to create a story around it. People love stories! And remember to repeat the message that you want to get across a few times! Not just once!

2. You May Need a Mentor
Sometimes you get too sucked in in your own presenation that you might miss the bigger picture. Having a mentor or colleague to show your slides a few days before your talk is a great idea. Most of the times you get excellent feedback that you can use. Also, see what others are doing. Establish connections. Having a mentor will help you refine your skills.

3. The Target Audience
Know what your target audience is before you start writing your presentation. Each group of people will have to be approached in a specific way. If you have no idea who will be receiving your speeches, you will fail making those highly specific and relevant.

4. Work on Your Public Speaking Skills
Even if you have the best personal stories and lessons to share, you will fail due to poor speaking skills. Work hard on mastering your public speaking. The best way to see what you are doing is to videotape your speeches. Once you do it, watch the records very carefully. Pay attention to your intonation, your body languages and the eye contact you establish with the audience (this is very important!). Learn how to sound natural and reassuring. If you need to, enroll in a public speaking course that will help you polish your skills.

5. Be enthusiastic
I cannot stress enough the value of being enthusiastic. If you are not enthusiastic about your results and presentation, don't expect others to be enthusiastic. Remember: you are presenting unique results that you have worked hard for! There is a special message to deliver and you are the first person to ever pass this message across!

6. Understand Your Audience’s Feedback
Good presenters listen to their audience. Learn how to ask for feedback and how to listen to the things that people have to say. The easiest way to receive some information is through the creation of a simple poll. Be ready to modify anything that seems to be failing. Also, be enthusiastic about your feedback, NOT angry or disappointed! People have taken the time to listen to you and want to help you improve the weak points so that next time you will be better and better.

7. A Good Speaker is a Good Writer
Publish articles and informative pieces in blogs, websites and specialized magazines. Apart from being a good form of publicity, it will help you master your motivational speaking skills. A good speaker is a good writer, as well. Learn how to master both.

8. Be Flexible!
The most important rule for any professional is to maintain a degree of flexibility. Be ready to change parts of your speech at any time. Do not become emotionally attached to your talk as the things you considered successful may fail influencing your audience. Next time, try a different approach.

9. Know your stuff
Make sure you know what EVERY SINGLE WORD on your slides mean as well as the principle behind each central concept that you are using (i.e. what is the principle behind minimization or molecular dynamics?). Remember, you are on the spot up there and never know what people may ask you.

9. Acknowledge
It is ABSOLUTELY NECESSARY to include an acknowledgement slide at the end of your presentation no matter how formal or informal your seminar is. Who provided you with data? Who helped you with your research or by discussing critical aspects of the project? Who are your collaborators?

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Before:

1. In the address line, type in "about:config" (without quotation marks). Click on "I'll be careful, I promise!"

2. In the filter field, type in browser.showQuitWarning. This should filter out all other options

3. Double click on the option that is left in the list. The value should switch from "false" to "true".

4. Close about:config tab and it should work

Taken from: http://www.virtualhelp.me/applications/51-office/288-firefox-4-doesnt-save-tabs

To install/Update Nvidia card drivers open Terminal (Press Alt+F2 and type: gnome-terminal) and copy the following commands in the terminal:

sudo apt-add-repository ppa:ubuntu-x-swat/x-updates
sudo apt-get update
sudo apt-get install nvidia-current When installation complete restart your PC. Now to check the installation is successful Press Window/Super key and type: nvidia x server settings and open it.

Taken from http://www.noobslab.com/2011/09/nvidia-drivers-for-ubuntu-1110-oneiric.html

A very recent paper, where the authors use an impressive combination of multiple docking programs (FlexX, eHiTS, Glide, AutoDock-Vina) and sub-terms of their scoring functions to identify new inhibitors of a Potassium Channel. It is also noteworthy that among all docking programs AutoDock-Vina achieved the best enrichment as shown by the ROC curves.

Wacker SJ, Jurkowski W, Simmons KJ, Fishwick CW, Johnson AP, Madge D, Lindahl E, Rolland JF, de Groot BL., "Identification of Selective Inhibitors of the Potassium Channel Kv1.1-1.2((3)) by High-Throughput Virtual Screening and Automated Patch Clamp.", ChemMedChem. 2012 Mar 30.

PMID: 22473914

AutoDock is a commercial-free suite of automated docking tools. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina.

AutoDock has its own suite for receptor and ligand preparation:

http://mgltools.scripps.edu/

, as well as for Virtual Screening:

http://pyrx.sourceforge.net/

It has also been recently enriched with new scoring functions derived from neural networks:

http://www.nbcr.net/software/nnscore/

AutoDock can also be run in parallel on the web:

http://www.worldcommunitygrid.org/

https://www.nbcr.net/pub/wiki/index.php?title=CADD_Pipeline

There is also a bootable, self-configuring system for virtual screening, which can run AutoDock on multiple PCs that are not necessarily connected by a queueing system:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987878/

AutoDock has also its own PyMOL plugin:

http://wwwuser.gwdg.de/~dseelig/adplugin.html