Hi,
On Wed, Sep 25, 2013 at 8:17 AM, Concha, Monica
<Monica.Concha.ars.usda.gov> wrote:
> I am trying to generate the topology file for a molecule of 8 glucose residues with 3 peptides attached to it. My purpose is to build a cellulose nanocrystal with peptides and minimize and carry out an MD simulation with Amber software.
> I gave the following command:
> antechamber -i new-chemx.pdb -fi pdb -o new-chemx.mol2 -fo mol2 -c bcc
> And I got the following error messages:
> The atom number exceeds the MAXATOM, reallocate memory
Antechamber is only intended to be used to develop parameters for
small molecules or building blocks that can be used to create large
molecules (such as individual amino acids etc); you should not be
using it to develop parameters for a complex molecule. You should just
use tleap with the GLYCAM forcefield for the sugar parameters and
ff12SB for the peptide parameters (or another protein FF if you
prefer). See chapters 2 and 4 in the AmberTools 13 manual, as well as
Amber tutorial B1 for more information. Also, the GLYCAM Biomolecule
Builder may be of interest to you:
http://glycam.ccrc.uga.edu/ccrc/biombuilder/biomb_index.jsp
Good luck,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Sep 25 2013 - 08:00:05 PDT
