Re: [AMBER] about sybylmol2 file

From: Jason Swails <>
Date: Thu, 10 Jun 2010 20:14:46 -0400


Why are you trying to convert to a mol2 to a prepin? Both carry the same
information and can be used in the same way with leap. I will include more
comments below...

On Thu, Jun 10, 2010 at 10:33 AM, Navanath Kumbhar <>wrote:

> Dear Sir,
> I want to creates .prepin and frcmod files for modified nucleosides by
> using
> antechamber, for that i have taken sybylmol2 file as input for
> antechamber,
> but it gives error as follows:
> $ antechamber -i wym.mol2 -fi mol2 -o wym.prepin -fo prepi -c bcc -s 2
> The atom number exceeds the MAXATOM, reallocate memoryRunning:

How big is this mol2 (i.e. how many atoms?) Antechamber is not meant to
deal with very large systems...

> /usr/local/amber10/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Running: /usr/local/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Total number of electrons: 1383; net charge: 0
> INFO: Number of electrons is odd: 1383

This is strange, and will only happen with an open-shell system
(obviously). mopac cannot handle open-shell systems as far as I know.
Furthermore, the spin multiplicity cannot be 1 if the electron number is
odd. Make sure all of the hydrogens are there where they should be.

> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
> Running: /usr/local/amber10/bin/
> Error: unable to find mopac charges in mopac.out
Good luck!

> So please give me any suggeastion for that.
> Thanks you
> Navanath Kumbhar
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jun 10 2010 - 17:30:05 PDT
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