Hi,
My name is Cathy. I'm a
new user of Modeller, and I'm still trying to figure out the input files to run
Modeller. I'm having trouble with the atom files...I don't exactly know what is
an atom file.
I tried using the .pdb file straight from the PDB. I tried changing
the file content to just the "atom" section of the PDB files. And nothing seems
to work.
I have the script file
& alignment file in the default Modeller directory, and I set the atom file
environment to a folder named "atom_files" with the 2 atom files (1pme &
1wbn). But when I try running my script, it says that atom files cannot be found
in the directory atom_files. Here's the exact error message:
====================
Read the alignment from
file : 1pme_1wbn.ali
Total number of
alignment positions: 388
#
Code #_Res #_Segm
PDB_code
Name
-------------------------------------------------------------------------------
1 1pme
380 1
1pme
2
1wbn 360
1 1wbn
runcmd______>
alignment.check()
check_a_343_> >>
BEGINNING OF COMMAND
openf5__224_>
Open 11 OLD SEQUENTIAL
\Modeller8v2\atom_files\1pme.atm
rdpdb___303E> No atoms were read from the
specified input PDB file, since
the
starting residue number and/or chain id in MODEL_SEGMENT
(or
the alignment file header) was not
found;
requested starting position: residue number " 0", chain " "
rdabrk__288W>
Protein not accepted: 1
1pme
check_a_337E> Structure not read in (please consult the log
file
for more details): 1
1pme
====================
It would be great if
anyone can help me with this problem! Thank you very much for your
time!
-
Cathy