Thank you sir.
The system is an Inorganic-Organic hybrid periodic material.
I wanted to get the connectivity information by generating topology file
for the system. I know the charges on the atoms.
I am not thinking of performing any simulations on this system as of now.
If you know any way of knowing the connectivity please let me know. Thanks.
with regards,
On Thu, Dec 15, 2011 at 12:43 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chidambar k
Int.PhD
JNCASR
Bangalore
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 14 2011 - 12:00:03 PST
