AMBER Archive (2006)

Subject: Re: AMBER: bond information in amber

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu May 11 2006 - 13:36:18 CDT

thanks a lot navin. I have CA, calcium atom present in my PDB. I also made
a lib, CA.lib and try to link it with the residues in PDB file.
The CA atom is linked to OD1 and OD2 atoms of the PDB residues. So when I
try to link CA atom to PDB residues it is giving me
following error message. Any help how can I fix it. The bond link between
CYS is working fine but it is giving me error message
while linking CA, calcium to OD1 and OD2 atoms.
Here is the message :
Checking for bond parameters.
Could not find bond parameter for: O2 - CA
No bond parameter for: O2 - CA
Could not find bond parameter for: O2 - CA
No bond parameter for: O2 - CA
Could not find bond parameter for: O2 - CA
No bond parameter for: O2 - CA
Could not find bond parameter for: O2 - CA
No bond parameter for: O2 - CA
Could not find bond parameter for: O2 - CA
No bond parameter for: O2 - CA
Checking for angle parameters.
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: C - O2 - CA
Can't find angle parameter: C - O2 - CA
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: C - O2 - CA
Can't find angle parameter: C - O2 - CA
Could not find angle parameter: C - O2 - CA
Can't find angle parameter: C - O2 - CA
Could not find angle parameter: O2 - CA - O2
Can't find angle parameter: O2 - CA - O2
Could not find angle parameter: C - O2 - CA
Can't find angle parameter: C - O2 - CA
Could not find angle parameter: C - O2 - CA
Can't find angle parameter: C - O2 - CA
There are missing parameters.

thanks in advance
snoze

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