AMBER Archive (2009)

Subject: Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Dec 29 2009 - 21:40:26 CST

On Tue, Dec 29, 2009, Alan wrote:
>
> This used to work pretty fine with AT 1.2, without any warning, but now with
> AT 1.3 ...:
>
> - Extract ligand DMP from 1BVG, name it Ligand.pdb
>
> - Enter sleap terminal command and enter:
> [gtkleap]$ source leaprc.ff99SB
> [gtkleap]$ source leaprc.gaff
> Info: ignoring unknown atom type: h
> Info: while reading ANGL. Input: f c h 51.5 109.90 SOURCE2
> 1 0.0000 0.0000

The warnings are genuine but innocuous-- there are some inconsisent
entries in the gaff database.

>
> [gtkleap]$ set default fastbld on
> [gtkleap]$ DMP = loadpdb Ligand.pdb
> Warning: cannot find template for residue DMP in our library.
> You will not be able to save prmtop for this molecule.

This is a genuine problem. Through an oversight, the tests for fastbld and
related components of sleap were not included in the automatic test suite, and
no one noticed that they were broken. We'll post a bug-fix when we figure
this out. In the meantime, try either going back to AmberTools 1.2, or running
the steps by hand with antechamber.

Thanks for the report....dac

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