On Wed, Dec 14, 2011, Chidambar Kulkarni wrote:
> I am using AmberTools 1.5 to generate the .mol2
> file for a system containing 5040 atoms. But the generation of the .mol2 is
> failing with an error (given below)
> The atom number exceeds the MAXATOM, reallocate memory
> Running: /home/chidambar/softwares/amber11/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
First, these are not errors, just informational messages.
Second, antechamber is designed to produce library files for small organic
molecules, containing maybe a few hundred atoms. (Junmei: we really need to
revise the Users' Manual introduction to antechamber to make things like this
clear.) You will need to divide your 5,000 atom system into smaller
fragments, then use LEaP to re-combine them back into a macromolecule.
...hope this helps....if you have more questions, please try to indicate what
kind of a molecule you are working with, and what you plan to do with the mol2
file if/when it gets generated.
....dac
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Received on Wed Dec 14 2011 - 11:30:03 PST
