VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 23 2015 - 06:43:51 CDT

On Tue, Jun 23, 2015 at 6:16 AM, Kin Leung CHU <klchuaa_at_connect.ust.hk> wrote:
> Dear All,
>
>
> I have a problem with topotools while dealing with my files with >10k atoms.
>
>
> I have a system of several layers of graphene (PDB generated from Nanotube
> Builder in VMD) which contains >10k atoms.
>
>
> When I use topotools to generate the PSF file from this PDB, the residue
> number messes up after 9999 (it somehow restarts from 271 and then to other
> strange numberings)

you can write out a psf directly after the nanotube builder has run.
why save the pdb (which loses the topology information) and then try
to regenerate it?