From: Kin Leung CHU (
Date: Tue Jun 23 2015 - 05:16:53 CDT

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).

After that, when I merge it with some protein using psfgen, the whole sheets have distorted very badly (and I suspect it was the problem from topotools previously).

I wonder what can I do to solve the above problems?

Thank you very much.


Kelvin Chu