Re: [AMBER] maximum number of atoms

From: Marc-André Dubois <>
Date: Thu, 20 Jan 2011 18:36:42 -0500

            Thank you very much for your reply. I will try to break the organic molecule as you suggest. I don't why however SQM seems to take a lot of time comparing with MOPAC..

Le 2011-01-20 à 18:26, Jason Swails a écrit :

> Hello,
> On Thu, Jan 20, 2011 at 5:47 PM, Marc-André Dubois
> <>wrote:
>> 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),
> Jason
>> Marc-André Dubois
>> Université de Montréal
>> _______________________________________________
>> AMBER mailing list
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list

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Received on Thu Jan 20 2011 - 16:00:06 PST
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