VMD-L Mailing List

From: Mamta Mohan (mamta_mohan_at_comcast.net)
Date: Thu Sep 18 2008 - 10:11:33 CDT

Dear VMD Team,

I am trying to generate psf file for a protein. I got following warning. Topology file used is the one which vmd loads as default.

Warning: failed to set coordinate for atom O SER:141 STN
Info: guessing coordinates for 1159 atoms (15 non-hydrogen)
Warning: poorly guessed coordinates for 7 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 LYS:6 STN
Warning: poorly guessed coordinate for atom HT2 LYS:6 STN
Warning: poorly guessed coordinate for atom HT3 LYS:6 STN
Warning: poorly guessed coordinate for atom HG2 PRO:42 STN
Warning: poorly guessed coordinate for atom HG2 PRO:56 STN
Warning: poorly guessed coordinate for atom OT1 SER:141 STN
Warning: poorly guessed coordinate for atom OT2 SER:141 STN

Could you please explain why they are showing up. Are they normal or could they cause some issue while I run a simulation on the protein.

Thank you.
Mamta Mohan