Re: [AMBER-Developers] sleap -> tleap migration

From: Wei Zhang <>
Date: Fri, 18 May 2012 13:29:06 -0500

Hi All,

    As Lachele pointed out, sleap is buggy at this point and it not ready
for use.

    Our plan is that Qian will do most of the development work and I will
instruct. This time
we will be very careful and make sure that sleap generates exact same
prmtop as tleap does.



On Mon, May 14, 2012 at 5:34 PM, Eric Pettersen <> wrote:

> On May 10, 2012, at 6:53 PM, case wrote:
> Why not stick with sleap? I don't know of any incompatibilities. I'm
> cc-ing
> this to Wei (who may not follow the developers list) to see if he has
> ideas.
> I'm not sure how hard it might be to port the parmeter checking code into
> the
> tleap code base.
> Hi Dave,
> Are you suggesting sticking with AmberTools11, or instead using
> AmberTools12 but copy sleap into it? If the former, then obviously I
> wouldn't benefit from any improvements to antechamber/sqm [which Chimera
> also uses] and wouldn't be able to offer the new ff12SB force field. If
> the latter (assuming that would work), there'd still be the drawback that
> generated prmtop files wouldn't have any of the new sections that tleap
> writes, but maybe that's not a big deal -- I don't know....
> On May 11, 2012, at 7:45 PM, Wei Zhang wrote:
> Hi Eric,
> I also think stick to sleap a better solution, at least for now.
> Other than parmchk, sleap does many things to work with Chimera,
> especially for the mol2 format, which cannot easily be ported to tleap.
> I am CCing this to Qian Zhang, who is a Ph D. student in Suchow
> University
> in China and has spent quite some time on sleap code, and is willing to
> contribute
> to sleap and make it better. I am thinking that he can take over the
> project with
> my help.
> Hi Wei/Qian,
> Well if sleap continued to be developed/offered obviously that would be
> easiest for me. Would the plan be to integrate it back into AmberTools at
> some point, or to offer it as a separate package/download?
> You are right about tleap and mol2. I did some of the work on the
> conversion to Amber12 before running into the parmchk thing, and for
> Solvate I had to change to providing PDB as input for tleap since tleap had
> no idea what the atom types were if I provided mol2.
> --Eric
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Received on Fri May 18 2012 - 11:30:03 PDT
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