AMBER Archive (2007)

Subject: Re: AMBER: Prepin error (?) in xleap

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 27 2007 - 10:58:20 CDT

On Fri, Aug 24, 2007, Lili Peng wrote:

> I created it using prepgen in antechamber:
>
> "prepgen -i glu3.ac -o glu3.prepin -f int -rn GLU3 -rf GLU3.res"

There could be a problem with prepgen here, but my best guess is that you
don't really want to run this program anyway.

If you want to make a GLU3 residue, you probably want to just use antechamber
itself, starting (probably) from a pdb file, and ending up with a mol2 file.
Something like this:

   antechamber -fi pdb -i glu3.pdb -fo mol2 -o glu3.mol2 -c bcc

If your GLU3 residue has a non-zero net charge, you will also need the "-nc"
flag.

This path ensures that you get gaff atom types. It looks like you are
creating files with tripos or insight atom types. Antechamber doesn't care
if you do this, but LEaP won't accept them, as you have seen.

...dac

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