AMBER Archive (2007)

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

From: Junmei Wang (junmwang_at_yahoo.com)
Date: Mon Aug 27 2007 - 17:17:53 CDT

I found your mol2 and pdb files do not contain hydrogen atoms. Antechamber only works for molecules without open valences.

Best

Junmei

Lili Peng <lilipeng_at_gmail.com> wrote: 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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