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

From: Eric Pettersen <>
Date: Wed, 16 May 2012 17:02:28 -0700

The mail server I use was sick yesterday and rejected some messages it
shouldn't have, in case there was a reply I missed...
[if there wasn't, please don't interpret this as whining! :-) ]


On May 14, 2012, at 3:34 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 Wed May 16 2012 - 17:30:03 PDT
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