I encountered a similar problem before. It may that H100 has one too many letters for the residue tag. Reduce the residue tag to 3 characters. For instance, try HA0 for H100, OA1 for O101, HA2 for H102 etc..
________________________________________
From: Joaquin Barroso Flores [joaco_barroso.yahoo.com]
Sent: Thursday, October 25, 2012 7:26 PM
To: amber.ambermd.org
Subject: [AMBER] Error 'Created a new atom named:'
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 - 19:00:03 PDT
