AMBER Archive (2008)


From: M. L. Dodson (
Date: Mon Dec 15 2008 - 11:52:48 CST

Ross Walker wrote:
> Hi Francois,
> I think Brent addressed some of your earlier questions and comments. I just wanted to follow up on a couple of these.
>> - Concerning required tutorials for charge derivation at the AMBER web
>> site, One might decide to update some web pages allowing the AMBER
>> community to easily find the tutorials (only
>> about charge derivation & force field library building) @
>>, and to find R.E.DD.B. which
>> does not exist! I have no problems to
>> help/participate/whatever_the_word_is, however, may be using what is
>> already available might be a good start.
> I agree that as it stands right now it is not obvious that R.E.DD.B. exists from the aspect of the AMBER website and I think it would be great if this was address. In fact if the use of RED for charge derivation is the recommended way to go with generating charges for the AMBER force fields, which I assume it is since you and Piotr developed it together, then really it should be better advertized from the AMBER site and in some ways integrated into the AMBER tutorials slightly better.
> For example if you would be kind enough to re-write section 1 of the Tutorial A1 to use R.E.D. then I would be more than happy to include this in the tutorial in place of what is currently there and then update the remainder of the tutorial to use those files. It would be great to have a tutorial on the AMBER site that shows how 'modern' charge derivation should be done (at least in an introductory fashion) in a way that couples it in with building a system from scratch. It can then of course include links to more complex examples / considerations.
> With regards to discussion of R.E.D. on the AMBER website you are welcome to update this. Just send me (via personal email) your public ssh key and your preferred username and I can give you access to the AMBER web CVS where you can modify any out of date descriptions / links etc.
> Thinking longer term would it not make sense for R.E.D. to be
> included in AmberTools? Dave Case would have to comment here but it
> seems to me that at least in some form, even if it was just an empty
> directory with README's in etc it would make sense. The biggest
> issue right now, from what I can see is that it is not clear, to and
> end user, how R.E.D. integrates into AMBER charge generation. There
> are multiple ways to do charge fitting using RESP etc etc that just
> serves to confuse people. If you (and other AMBER people) think that
> we should consider standardizing on R.E.D. then it would be good if
> it can be more closely integrated within the AMBER Tools
> distribution and thus discussed in detail in the manual, with an
> example in with the AMBER tutorials and then with links to the
> R.E.D. site for more detailed information.

I think the R.E.D. license is completely incompatible with the
AmberTools license. Of course, people who write software have the
complete right to put whatever license they wish on their work
product, so I am not complaining about that. I just think the
AmberTools project is in the best tradition of academic research and
would like to see it promoted, but R.E.D., based on its license, is
not working toward the same end. In my opinion, of course.

Bud Dodson

>> - Finally, yes, writing tutorial takes time, you are right. With Piotr
>> we have read & re-read our 2 tutorials @
>> Other people here have also
>> read them to help. Personnally, I prefer releasing nothing than
>> something I do not master, & let others more qualified explain what
>> they know.
> I agree - if you can find that someone who is an expert to donate their time - otherwise nothing gets done or it all just gets done piecemeal with no coherent structure. At some point somebody just has to bite the bullet and make their best attempt to put together something that will be useful to beginners.
> My point is that you obviously understand charge fitting far more than I do so I would love it if you could donate the time to update the tutorial.
> All the best
> Ross

M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
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