On Mon, May 14, 2012, Eric Pettersen wrote:
> 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....
>
> 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.
Can you elaborate? This doesn't (seem to) accord with my experience: the
loadMol2 function in tleap pulls in atom types correctly, at least for me.
But maybe the mol2 files I'm using are different from the ones you have(?)
Generally, I'd think that copying sleap into AmberTools12 ought to mostly
work. Of course, it would be great if good features of sleap could be ported
to tleap; (or vice-versa, but [as we have seen], keeping two versions of the
LEaP functionality in sync requires a real development commitment.).
...regards...dave
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Received on Thu May 17 2012 - 06:30:03 PDT
