Re: [AMBER-Developers] Experiences with sleap

From: Eric Pettersen <>
Date: Fri, 4 Nov 2011 13:19:42 -0700

On Nov 3, 2011, at 8:16 PM, case wrote:

> On Thu, Nov 03, 2011, Eric Pettersen wrote:
>> 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.
> This is good to know, since the command files for tleap and sleap are
> indeed nearly identical. And tleap is a very "clean" build (ANSI C
> with
> no dependencies, and code that changes only rarely), so a switch-over
> might be fairly straightforward. (If you got "Dock Prep" to work,
> tleap
> should be a piece of cake.)

I'm hoping so! :-)

> Does the Tools -> Structure Editing -> AddH routine use Wei's
> code? Does
> anything else?

The tools that Wei contributed and that interface with sleap are all
in the "Amber" category (i.e. Add Ions, Add Solvent, and Write
Prmtop). If adding hydrogens via sleap/tleap (instead of via
Chimera's AddH) was needed for some reason, it could probably be added.

The other part of Chimera that uses Amber extensively is the Add
Charge tool. It assigns charges to standard residues (cribbed from
*amino/nucleic*.lib files) with a choice of various force field
versions (ff99SB, etc.), and also uses antechamber/sqm to assign
charges to non-standard residues / small molecules.

I haven't yet investigated getting Chimera to directly link to SFF
routines in order to more closely integrate minimization, etc. as per
our discussion when you were here awhile back.

> I really need to free up time to learn Chimera better, especially
> the "Build
> Structure" tool. But I suspect that there are still times when I
> will use
> xleap for interactive structure building, just because I am so
> familiar with
> it (quirks and all).

Yeah, it's hard to get motivated to learn a new tool when the old tool
already does what you want. Frequently cattle prods are necessary.


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Received on Fri Nov 04 2011 - 13:30:06 PDT
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