VMD-L Mailing List

From: Sergio Anis (sergioanis_at_ispwest.com)
Date: Wed Sep 14 2005 - 06:06:48 CDT

i re-check the CONECT statements and found out some mistakes, there are some 'dangling' atoms. i guess that they are responsible for the error messages 'exceeded number of bonds' since the software is not able to tell if they belong to the protein or the heterogroup.

thanks for your help
Sergio

----- Original Message -----
From: Dow Hurst DPHURST
Date: 09/13/05 16:16:12
To: Sergio Anis
Subject: Re: vmd-l: writing pdb
 
 
 
 
 
Not necessarily, it depends on how the code is designed to interpret the
PDB file. If no connectivity information is included in the PDB file and
also if the program uses topology files as a reference, then you might not
see anything or just unconnected dots. PDB is great for well defined
proteins but can give problems with small molecules and so on.
Dow