AMBER Archive (2006)

Subject: RE: AMBER: NEWPDB.PDB from antechamber

From: Junmei Wang (jwang_at_encysive.com)
Date: Wed Nov 01 2006 - 11:19:27 CST

Hi, Esther
You should use the file specified with flag "-o", NEWPDB.PDB is a
intermediate file and may be useful for debugging purpose.
 
All the best
 
Junmei
 
 

        -----Original Message-----
        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
On Behalf Of Esther Brugger
        Sent: Wednesday, November 01, 2006 10:59 AM
        To: amber_at_scripps.edu
        Subject: AMBER: NEWPDB.PDB from antechamber
        
        
        Hello everyone,
        
        I am using the antechamber to calculate the charge. I checked
the divcon.out file, it seems everything is OK. But when I load the
output file "NEWPDB.PDB" in xleap or VMD, I found the structure is not
corret, it is a littlbe bit mess up. Do you think is there something
wrong there? If I load the initial pdb file with the prepin and frcmod
files in xleap, it is no problem. Do you think I can still use the
initial pdb file to do the other calcuations? Thanks a lot for your
help!
        
        Bests,
        Esther B.
        
        
        

        
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