AMBER Archive (2006)

Subject: RE: AMBER: NEWPDB.PDB from antechamber

From: Esther Brugger (
Date: Wed Nov 01 2006 - 13:10:20 CST

Thanks for your answer. I understand it now. But after the calculation, only in the output file "divcon.out", it has the coordinates for the molcules. But when I extracted these coordinates in a new pdb file, the structure is better, but still some parts are messed up. Is there something wrong there? Maybe I didn't understant is clearly.
 Thank you very much!

Junmei Wang <> wrote:Message 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

    -----Original Message-----
From: [] On Behalf Of Esther Brugger
Sent: Wednesday, November 01, 2006 10:59 AM
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!

Esther B.


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