The Molecular Graphics Laboratory Forum
http://mgl.scripps.edu/forum/

Input for future features of AutoDock, Vina & ADT
http://mgl.scripps.edu/forum/viewtopic.php?f=26&t=1331
Page 2 of 2

Author:  dmcancw [ Wed Mar 09, 2011 2:01 am ]
Post subject:  Re: Input for future features of AutoDock, Vina & ADT

Thank you for the thoughtful R&D on this AutoDock n ADT.
I myself is a beginner in autodock and I find it a bit difficult to learn from the AutoDock based on the current autodock tutorial guides and the forum, especially from a student who has limited knowledge of bioinformatic and molecular dynamic.
I tried the tutorial, reading forums and even consult people from my university who claimed did AutoDock before (they are not much friendly in teachings, maybe because they feel i am going into their field and they feel insecure in that). I was asked to refer to forum when i am so depress of looking for solution on my doubts. in which the forum was too many jorgan and technical discussion,and I still find no answer to my question. I never expect this to come in easily, however, I felt lost in learning this programme.

Yes, i do find alot of difficulty in learning it. Thus I shifted to other docking softwares in the market. Their tutorials are more user-friendly(at least to me), in which it explains clearly why you need to perform certain steps, how do you alter the steps according to your own needs (your own compounds) and it also gives immediate troubleshooting feedback on errors i did, both from the technical support team as well as the software itself.

However, having said so, I have not stop learning autodock, as I believe this is a good validated software. If the team is looking for improvement in this programme, i am very happy to look forward for improvement in existing software to a much user friendly, step-by-step guided autodock tutorial. Maybe is too much to ask, however I do appreciate the improvement to help more beginners, and those who faced doubts in the softwares

Author:  oleg_trott [ Thu Mar 10, 2011 5:34 pm ]
Post subject:  Re: Input for future features of AutoDock, Vina & ADT

dmcancw wrote:
Thank you for the thoughtful R&D on this AutoDock n ADT.
I myself is a beginner in autodock and I find it a bit difficult to learn from the AutoDock based on the current autodock tutorial guides and the forum, especially from a student who has limited knowledge of bioinformatic and molecular dynamic.
I tried the tutorial, reading forums and even consult people from my university who claimed did AutoDock before (they are not much friendly in teachings, maybe because they feel i am going into their field and they feel insecure in that). I was asked to refer to forum when i am so depress of looking for solution on my doubts. in which the forum was too many jorgan and technical discussion,and I still find no answer to my question. I never expect this to come in easily, however, I felt lost in learning this programme.

Yes, i do find alot of difficulty in learning it. Thus I shifted to other docking softwares in the market. Their tutorials are more user-friendly(at least to me), in which it explains clearly why you need to perform certain steps, how do you alter the steps according to your own needs (your own compounds) and it also gives immediate troubleshooting feedback on errors i did, both from the technical support team as well as the software itself.

However, having said so, I have not stop learning autodock, as I believe this is a good validated software. If the team is looking for improvement in this programme, i am very happy to look forward for improvement in existing software to a much user friendly, step-by-step guided autodock tutorial. Maybe is too much to ask, however I do appreciate the improvement to help more beginners, and those who faced doubts in the softwares


Hi,

You may want to try the video tutorial for AutoDock Vina: http://vina.scripps.edu/tutorial.html . It does attempt to explain the "why" before showing the "how". I also recommend reading the "Intro" and "Theory" parts of the Vina paper, if you are interested in the background.

Oleg

P.S. This thread is set to expire soon, and will be moved to "Announcements" rather than being global.

Page 2 of 2 All times are UTC
Powered by phpBB® Forum Software © phpBB Group
https://www.phpbb.com/