AMBER Archive (2007)

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

From: Lili Peng (lilipeng_at_gmail.com)
Date: Mon Aug 27 2007 - 16:38:30 CDT

Hi Dr. Case,

Thanks for your reply. I tried running antechamber initially (as you
prescribed), but my converted mol2 file is really weird. The carbon atoms
get converted to Californium and Cerium atoms. There's even a Neon atom in
the structure, as well as many "Unknowns". I have no idea how the carbon
atoms got converted into them.

I have attached the original PDB and mol2 files for your convenience.

Thanks,
Lili

On 8/27/07, David A. Case <case_at_scripps.edu > wrote:
>
> 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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  • application/octet-stream attachment: glu3.mol2
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