On Thu, May 10, 2012, Eric Pettersen wrote:
> So I'm trying to move Chimera from Amber(Tools) 11 to 12, which means
> using tleap instead of sleap. It turns out that sleap has one
> critical function (for writing prmtop files) that tleap lacks: a built-
> in parmchk command. What this does (in sleap) is find residues with
> missing parameters, and run the external parmchk command on each of
> the residues in turn and read the parameters back in. Without it,
> tleap simply complains when there are missing parameters and refuses
> to write out a prmtop file. Running parmtop externally on the entire
> structure is not really an option since even on a small protein (1gcn,
> 29 residues) parmtop takes over 11 minutes to run (even though no
> parameters are actually missing)! Not to mention that the structure
> could have mixed standard Amber atom types and GAFF types (homogenous
> on a per-residue basis though) and I would therefore need to
> concatenate together the appropriate GAFF/AMBER parameter files and
> get parmchk to use that.
> I guess I'm looking for advice on any functionality I may have missed
> that would make life easier here. The only workaround I can think of
> is to have Chimera run parmchk on each residue that uses GAFF types
> (since Chimera has no way of knowing if parameters are missing). This
> would still be problematic for structures with mixed polymeric
> standard and non-standard residues, but sleap didn't handle those
> either.
> So, any other ideas?
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.
....regards....dave
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Received on Thu May 10 2012 - 19:00:05 PDT
