Re: [modeller_usage] nselat__596E> Atom index is out of range (iatm, natm)
To: MGiò <>
Subject: Re: [modeller_usage] nselat__596E> Atom index is out of range (iatm, natm)
From: Modeller Caretaker <>
Date: Wed, 01 Mar 2006 12:23:10 -0800
Cc:
MGiò wrote:
I'm trying and model a 7-helix trans-membrane receptor, as I don't like
the way MODELLER models my helices, while I highly appreciate its loop
modelling, I've been using the "model-myini.py" input script to model my
receptor starting from a initial.pdb containing the 7 helices already
modelled. Every MODELLER run ends with the "nselat__596E> Atom index is
out of range" error. Considering that this error changes the couple of
atoms referring to any time I delete the corresponding residue in order
to by-pass the error. I've attached to the mail the input files I used
and the log file. Can you help me?
OK, looking at the full set of input files, the problem is clear. The
initial model you provide must match the sequence you're trying to
build, but in your case the sequence has 2871 atoms, while the
'helices.pdb' file you're providing as an initial model has only 1702. I
suggest you run your script again, but with the "inifile='helices.pdb'"
option removed, so that you get ordinary model building, and look at the
generated GHSR.ini initial model. Your helices.pdb file must have the
same number of atoms (in the same order).
I'll add some extra checks to the code in future so that you get a more
explanatory message than "atom index out of range".