Re: [AMBER-Developers] Experiences with sleap

From: Wei Zhang <>
Date: Wed, 2 Nov 2011 22:30:09 -0500

Hi All,

    When I started to write sleap in 2005, the original goal was to use it to
replace tleap, but after 6 years I have to admit that I have failed the goal,
    Yes, sleap is a failed product. I hate to admit it but it is true. It is unstable,
and does not work as expected. The most important thing is sleap does not
generate identical topology as tleap does, thus it is hard for user to tell if
the resulted topology file is correct or not which make it useless.

    Here I try to summarize the reasons why I have failed, maybe people can
benefit from my failures:

    The No 1. reason is: The need was unclear, i.e. why do we need a replacement
for tleap? tleap is a very well written piece of software, it has been working for
decades. It surely has some bugs, but the correct solution should be to fix those
bugs, not to write a new one.
    The No 2. reason is: I totally underestimated the difficulty of the project. That's
why even though I was not asked to do it, I did it anyway. When I started
writing sleap, I thought it would take me at most 2 months. It turns out to be much
more complicated than I thought. Now I recall that Dave tried to warn me about
the difficulty, but I was so reckless at that time that I disregarded his warning.

    The No 3. reason is: I did not know tleap well enough. This is related to
reason No. 2. Because I though it was an easy job, I did not spend enough time to
study the tleap code and tried to understand every line of it. I just started on
my own.

     These are the lessons I learned from development of sleap. At this point
I am not sure what to do with it, and I would really appreciate your advices.
I guess the most important question is: Do we really need a replacement for
tleap? or we just need to fix bugs of tleap?

     Thank you very much!


     Wei Zhang

On Nov 2, 2011, at 8:32 PM, case wrote:

> On Wed, Nov 02, 2011, Daniel Roe wrote:
>> I think the only major thing sleap does that tleap doesn't do is set
>> up parms for AMOEBA right?
> Please cc comments about sleap to Wei Zhang <>, since he may
> not always follow the mail reflector.
> Just a brief addition to Jason's post (and Wei can add more if he wants):
> There *was* an original intent to create a graphical interface for sleap
> (hence the directory name gleap, short for gtk-leap). But Wei later
> decided to use Chimera as the graphical interface, and there are now
> dropdown menus in Chimera that allow one to build prmtop files and to do
> most of the things that tleap does (and more).
> But it is the case that (a) only a few people use the Chimera interface;
> (b) Wei is basically the only person (maybe along with Eric Pettersen) who
> feels comfortable in maintaining the code, so it has languished. [This can
> be a cautionary tale to those of you (Dan, Dave C., etc.) who have "your"
> code: it may never really take off until/unless you make sure that others
> can understand it, can modify it, and actually use and "buy into" it.]
> Wei will be at the meeting in January, so we can discuss this then, but email
> information exchange prior to that is also encouraged.
> ...dac
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Received on Wed Nov 02 2011 - 20:30:02 PDT
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