[AMBER] Error 'Created a new atom named:'

From: Joaquin Barroso Flores <joaco_barroso.yahoo.com>
Date: Thu, 25 Oct 2012 18:26:03 -0700 (PDT)

Good day to everyone

I'm working with AMBER11 and I've run into a problem. My system consists of a host-guest complex in which host = macrocycle and guest = drug molecule. I'm able to generate the required parameters for both molecules but when I try to loadpdb the complex into tleap I get the following error:

Loading PDB file: ./aducto4.pdb
Created a new atom named: H100 within residue: .R<UNK 1>
Created a new atom named: O101 within residue: .R<UNK 1>
Created a new atom named: H102 within residue: .R<UNK 1>
Created a new atom named: O103 within residue: .R<UNK 1>
Created a new atom named: H104 within residue: .R<UNK 1>
... and so on for 27 atoms


the thing is that that the macrocycle has 126 atoms, this means there is clearly some error in my pdb which starts at the line where the 100th atom is, but I can't find it. This is an extract from my complex pdb file around where the error must be.
ATOM     98  H98 UNK     1      -9.549   7.116  -1.032  1.00  0.00
ATOM     99  O99 UNK     1      -6.061   1.783   7.940  1.00  0.00
ATOM    100 H100 UNK     1      -6.839   2.301   8.274  1.00  0.00
ATOM    101 O101 UNK     1      -0.319  -5.673   4.793  1.00  0.00
...
...
ATOM    125 H125 UNK     1      -1.314   3.985  -3.981  1.00  0.00
ATOM    126 H126 UNK     1      -2.993   4.208  -3.563  1.00  0.00
TER
ATOM    127  C1  IM      2      17.265  -2.336   2.811  1.00  0.00
ATOM    128  C2  IM      2      16.185  -2.472   3.683  1.00  0.00
ATOM    129  C3  IM      2      14.964  -1.879   3.360  1.00  0.00


Thanks in advanced for any help you might provide on this matter.

=======================================================

Joaquin Barroso-Flores, Ph. D.
Centro Conjunto de Investigacion en Quimica Sustentable
Instituto de Quimica
UNAM


-> http://joaquinbarroso.wordpress.com


joaquin.barroso''a''gmail.com


"Blogastronomía": http://joaquinbarroso.blogspot.com
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Received on Thu Oct 25 2012 - 18:30:03 PDT
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