On Wed, Oct 24, 2012 at 2:37 AM, ashley chen <ashley.huijia15.gmail.com>wrote:
> Hi,
>
> I have a question concerning the use of Antechamber. When I use the
> following command:
>
> antechamber -i 1EDG_reduce.pdb -fi pdb -o EDG.mol2 -fo mol2 -c bcc -s 2
> -nc -3
>
> I get errors:
>
> Running: /app1/linux/amber10a/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the actual number of rings (1094) exceeds the defaut ring size (500),
> reallocate memory automatically
> WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
> WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
> WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
> WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
> WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
> WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
> WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
> Total number of electrons: 22968; net charge: -3
>
You appear to be misusing antechamber. You should NOT use antechamber to
parametrize a system that has multiple amino acids (or, in fact, any
standard amino acids, as those are already parametrized).
Antechamber is designed to provide parameters for small organic ligands or
cofactors, not for extended biopolymers like proteins and nucleic acids.
If you have a small ligand in your PDB, you should create a separate PDB
that contains only those atoms from the ligand (note, ALL atoms must be
present, including hydrogens). You will then be provided with a library
file for this residue that you can load into tleap.
In tleap, the parameters and template for the ligand will be taken from the
files you created with antechamber, whereas all of the parameters and
templates for the standard amino and nucleic acids will be taken from the
templates and databases inside Amber itself.
HTH,
Jason
P.S., For clarity, please see the tutorials at
http://ambermd.org/tutorials
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Oct 24 2012 - 13:00:04 PDT
