[AMBER-Developers] sleap -> tleap migration

From: Eric Pettersen <pett.cgl.ucsf.edu>
Date: Thu, 10 May 2012 16:13:33 -0700

        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
        So, any other ideas?


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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Received on Thu May 10 2012 - 16:30:03 PDT
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