AMBER Archive (2008)

Subject: Re: AMBER: size of pdb

From: David A. Case (case_at_scripps.edu)
Date: Sat Jul 12 2008 - 09:45:51 CDT

On Fri, Jul 11, 2008, Boutheina Kerkeni wrote:
>
>
> I have a pdb fie containing 12180 atoms and 813 residues.
> When I load it to leap and add waters/
> solvateoct pdb TIP3PBOX 9.
> The newly solvated file contains more than 99999 atoms....
> and leap replaces the number of atoms beyond 99999 by stars.

This is a limitation of the PDB format. I think ambpdb "solves" this is in a
different way than LEaP does, so you might try that.

> I suppose the max number of atoms should not exceed 99999.

No, this is not true. However, if you are new to Amber, I would recommend
making sure that you are comfortable with smaller simulations (say 50-100
residues) before starting on such a big system.

...good luck...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu