From: Vermaas, Joshua (
Date: Wed Feb 13 2019 - 09:55:21 CST

Hi Ernest,

Its a pdb format restriction. pdb files can only have 4 characters for their residue id, so psfgen can get confused if there are more than 9999 residues. My usual way around this is to use topotools to merge together simulation systems. You'll want mergemols at the bottom of the page.


On 2019-02-13 05:14:00-07:00 wrote:

Dear VMD users,

I am using VMD for WIN32, version 1.9.3 (November 20, 2016). I am facing a problem whereby I cannot merge psf and pdb files using psfgen. I generated a carbon nanotube (>9,999 atoms) using the nanotube builder but I want to merge it with my other psf+pdb files. It seems to me that the key problem is the number of atoms generated for the carbon nanotube. If the number of CNT atoms is <10,000 atoms, psfgen works fine. The following is the excerpt of the generated pdb file for a CNT with >9,999 atoms. The numbering changes from 9999 to 2710... and this repeats what being numbered previously.

ATOM 9998 C CNT X9998 13.250 -2.816 304.550 0.00 0.00 TUB C
ATOM 9999 C CNT X9999 13.379 -2.119 305.778 0.00 0.00 TUB C
ATOM 10000 C CNT X2710 13.527 -0.709 305.778 0.00 0.00 TUB C
ATOM 10001 C CNT X2711 13.546 0.000 307.006 0.00 0.00 TUB C
ATOM 10002 C CNT X2712 13.471 1.416 307.006 0.00 0.00 TUB C

Can anyone help me to solve this problem?

Thank you.