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.
Sincerely,
Wei
On Mon, May 14, 2012 at 5:34 PM, Eric Pettersen <pett.cgl.ucsf.edu> 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
