AMBER Archive (2009)

Subject: Re: [AMBER] problem with parmchk

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Mon May 18 2009 - 09:34:31 CDT

Hello,
thanks for your answer. Actually, the system has only 264 rings, I don´t
know why antechamber thinks that it has 8616. The number of atoms is 312.
It is a carbon nanotube, consisting only in aromatic six member rings
joined to each other. Is this system too big to be parametrized by
Antechamber? Is there another way to do the parametrization for using GAFF
with this system?
Thank you very much for your help,
Best wishes,
Rebeca.

On Mon, 18 May 2009 10:19:54 -0400, "David A. Case"
<case_at_biomaps.rutgers.edu> wrote:
> On Mon, May 18, 2009, rebeca wrote:
>
>> I am trying to do some antechamber calculations for a CNT system. I
would
>> like to obtain the necessary files for using in xLeap (prep and frcmod).
>
>> Info: the atom number exceeds the MAXATOM, reallocate memory
>> automatically
>> Info: the actual number of rings (8616) exceeds the defaut ring size
>> (500),
>> reallocate memory automatically
>
> If you actually have something like 8616 rings(!) the system is way too
> big.
> Antechamber is designed for single residues, maybe 100 atoms at most.
>
>> Total number of electrons: 1752; net charge: 0
>
> This is also big, although way less than 8616 rings. Somehow,
antechamber
> is
> quite confused. See if you can divide your system into smaller pieces.
>
> ...dac
>
>
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-- 
Rebeca García Fandiño
Molecular Modelling and Bioinformatics Group
Institut de Reçerca Biomèdica 
Parc Cientific de Barcelona
08028 Barcelona
rebeca_at_mmb.pcb.ub.es

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