Re: [AMBER] Acpype error: Timed out process killed

From: Alan <>
Date: Mon, 22 Feb 2021 21:18:46 +0100

As Prof. Case said, you're playing off the limits.

Yet, ACPYPE has this option:

  -s MAX_TIME, --max_time MAX_TIME
                        max time (in sec) tolerance for sqm/mopac, default
                        3 hours
In my experience, ~250 atoms was already breaking the 10 hours limit (the
max I ever tested).

But you can try gasteiger:

  -c {gas,bcc,user}, --charge_method {gas,bcc,user}
                        charge method: gas, bcc (default), user (user's
                        charges in mol2 file)

It should work for a bigger system, yet it's not a semi-empirical
calculation like SQM.

My educated guess is that the charges for most of the tube would be regular
(with small variation possibly) except for the ends, so, you may try with
gasteiger and then try to replace the charges there following the profile
you see for a smaller tube you were able to run.

BTW, how many atoms did you get ACPYPE to work with? And how big is the one



On Mon, 22 Feb 2021 at 19:22, David A Case <> wrote:

> On Mon, Feb 22, 2021, Shilpa Gupta wrote:
> >I have run acpype for the generation of topology and coordinate parameters
> >for the nanotubes. For the smaller tubes (with less number of atoms) this
> >script is running fine but on increasing the size of the tube (with more
> >number of atoms) script is showing an error. Error is
> Antechamber is designed for small molecules, not for extended structures
> like nanotubes. You will probably need to divide your structure into
> smaller pieces, and assemble the bigger ones from smaller ones. See if you
> can find a paper that describes the force-field generation process for
> tubes that are similar to the ones you have.
> ...good luck....dac
> _______________________________________________
> AMBER mailing list

Alan Silva 🚲🏊‍♂🏃‍♂🇧🇷🇫🇷🇬🇧
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Received on Mon Feb 22 2021 - 12:30:03 PST
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