Re: [AMBER] maximum number of atoms

From: Jason Swails <>
Date: Thu, 20 Jan 2011 18:26:27 -0500


On Thu, Jan 20, 2011 at 5:47 PM, Marc-André Dubois

> Hi,
> I just started using AmberTools 1.4 and I am now able to successfully
> achieve some tutorials present on I try to
> repeat an exercise very similar to the B4 tutorial, but have some
> difficulties to complete the process. First, I am not able to run mopac with
> antechamber. I almost tried adding, but it is not functional. So I
> tried to run antechamber with sqm to get the charges, but I get a
> "segmentation Fault". My main concern is about the number of atoms of my
> organic molecule. The compound is a Trimer with a total of 230 atoms. Is
> there a limit in ambertools regarding the number of atoms? I also tried to
> calculate the charges

200 atoms is a large system to treat with quantum mechanics. One reason you
may have gotten a segfault with sqm is because your system doesn't have
enough memory to allocate to the job. In any case, this seems to be a very
difficult case for antechamber/sqm to handle. Perhaps you can break the
organic molecule down into individual "residues" (much like a protein is
broken down into amino acids) and parameterize each of those separately.

> using my own version of mopac, using mainly babel to convert my file in a
> mol2 file, but I still face a problem in the molecular dynamics. The
> movements seems erratic. Am I the first to face this situation? Thanks,

This is not terribly helpful. "Erratic" could mean many things. It could
be that you're just talking about periodic COM translation removal (to
eliminate drift). You should do some kind of RMS fit before really looking
at the dynamics so you know that translations and rotations aren't making it
'appear' worse than it is.

Also note that charge derivation is only one step of force field creation.
 You also need to make sure that you have the bond, angle, and (most
difficultly) the dihedral parameters. Dihedral parameters are the hardest
to get *right* since they're a correction term that are often misunderstood
(and you have the 1-4 scaling that complicates issues).

Hope this helps (a sqm/antechamber expert may interject here with more
helpful advice),

> Marc-André Dubois
> Université de Montréal
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jan 20 2011 - 15:30:02 PST
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