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 Mon May 14 2012 - 16:00:03 PDT
