VMD-L Mailing List

From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Wed Feb 13 2019 - 05:12:41 CST

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.

Regards,
Ernest