AMBER Archive (2006)

Subject: RE: AMBER: NEWPDB.PDB from antechamber

From: Junmei Wang (
Date: Wed Nov 01 2006 - 13:42:42 CST

Would you please send me your molecule? I can't figure out what happened
without the structure.
All the best
-----Original Message-----
From: [] On Behalf
Of Esther Brugger
Sent: Wednesday, November 01, 2006 1:10 PM
Subject: RE: AMBER: NEWPDB.PDB from antechamber

        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
        Thank you very much!
        Junmei Wang <> wrote:

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

                        -----Original Message-----
[] 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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