VMD-L Mailing List

From: Rangeen Othman (rangeen.othman_at_googlemail.com)
Date: Wed Nov 26 2014 - 09:20:10 CST

Dear VMD Users,

I have two structures (gold nano particle with lipid bilayer, pdb and psf
files) I want to combine them but it failed! I wonder if someone will
advise me what is the problem. Also I have checked that the system has
unique {segname resid name}. I have also used Topotool to merge them but
again it failed and complained with the same phrase!

psfgen) reading coordinates from pdb file mergetmp1312235701/2nmfix2.1s.pdb
psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A
psfgen) Warning: failed to set coordinate for atom AU1 AU:2 A
psfgen) Warning: failed to set coordinate for atom AU2 AU:3 A
psfgen) Warning: failed to set coordinate for atom AU3 AU:4 A
psfgen) Warning: failed to set coordinate for atom AU4 AU:5 A
psfgen) Warning: failed to set coordinate for atom AU5 AU:6 A
psfgen) Warning: failed to set coordinate for atom AU6 AU:7 A
psfgen) Warning: failed to set coordinate for atom AU7 AU:8 A
psfgen) Warning: failed to set coordinate for atom AU8 AU:9 A
psfgen) Warning: failed to set coordinate for atom AU9 AU:10 A
psfgen) Warning: failed to set coordinate for atom AU10 AU:11 A
psfgen) Warning: failed to set coordinate for atom AU11 AU:12 A
psfgen) Warning: failed to set coordinate for atom AU12 AU:13 A
psfgen) Warning: failed to set coordinate for atom AU13 AU:14 A
psfgen) Warning: failed to set coordinate for atom AU14 AU:15 A
psfgen) Warning: failed to set coordinate for atom AU15 AU:16 A
psfgen) Warning: failed to set coordinate for atom AU16 AU:17 A
psfgen) Warning: failed to set coordinate for atom AU17 AU:18 A
psfgen) Warning: failed to set coordinate for atom AU18 AU:19 A
psfgen) Warning: failed to set coordinate for atom AU19 AU:20 A

Thanks in advance

Rangeen