[gmx-users] Problems with a PDB

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Mar 18 20:28:10 CET 2005

does the pdb have CONNECT entries?
If the pdb has not this entries, when you read the file with VMD for e.g., the program does a distance search, and then draws the bonds between the atoms. If the structure is poorly defined, there's a great possibility of having wrong bonds on your display.

But, if you do a EM or small MD on the structure ....

  ----- Original Message ----- 
  From: Absalom Zamorano 
  To: gmx-users at gromacs.org 
  Sent: Friday, March 18, 2005 7:24 PM
  Subject: [gmx-users] Problems with a PDB

  HI gromacs-friends...Firstly thank you for your help in previous messages...Im starting in this forum and Its seems to me fantastic...
  Now another question... I have a pdb file and contains all the atoms that are theorically corrects. I mean the molecule is complete. But when I visualize this file with VMD  or VEGA, programs dont show all the bonds I expect. 
  I will appreciate your commentaries..

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