Re: [AMBER-Developers] Experiences with sleap

From: Eric Pettersen <>
Date: Thu, 3 Nov 2011 14:49:06 -0700

On Nov 2, 2011, at 6:32 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.]

I'm disappointed that sleap is languishing but I know that, as Wei
says, it's a very significant undertaking. Chris Schafmeister and I
hung out while he was implementing tleap and I know it took him many
months of dedicated work to get a useable implementation with basic

I'm familiar with the interface code between Chimera and sleap, but am
only marginally familiar with the sleap code itself. I'm comfortable
with modifying/improving the former and in no way could improve the
latter (even if my job description encompassed it)!

The way Chimera interfaces with sleap is that it writes an sleap
command file and invokes sleap with that command file, and then reads
back in any pertinent output files (for the add-ions and add-solvent
tools). So I guess my question is how compatible is the command
syntax between sleap and tleap? If the syntaxes are very similar it
should be easy to convert Chimera to using tleap if needed.

On Nov 3, 2011, at 11:28 AM, Wei Zhang wrote:

> Chimera is open source and free for academic use. On the other hand,
> incorporating tleap into VMD should not be very difficult either. Both
> Chimera and VMD were written in python.

Slight correction: VMD's command language is Tcl and it is mostly
written in that, though it also offers a Python interface.


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Received on Thu Nov 03 2011 - 15:00:04 PDT
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