To whom it may concern,
I'm a researcher of Naples University and I'm using modeller for my work. I've
followed correctly the Basic tutorial with my enzyme in the place of lactate
dehydrogenase. The program run but I got many warnings in the following .log
files:
1) when I run "mod8v0 compare.py" I got this warning:
fndatmi_285W> Number of residues <> number of atoms; atom code: 680
679 CA
2) when I run "mod8v0 align2d.py" I got these warnings:
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: N --> N
This message is written only for the first such atom.
fndatmi_285W> Number of residues <> number of atoms; atom code: 680
679 CA
fndatmi_285W> Number of residues <> number of atoms; atom code: 680
679 CA
3) when I run "mod8v0 model-single.py" I got these warnings:
fndatmi_285W> Number of residues <> number of atoms; atom code: 680
679 CA
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 275
atom names : C +N
atom indices : 2252 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 275
atom names : C CA +N O
atom indices : 2252 2247 0 2253
fndatmi_285W> Number of residues <> number of atoms; atom code: 680
679 CA
omgdel__425W> Unselected all O C +N +CA dihedrals: 282
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential
is used.
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 21721 19723
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to
handle
the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to
handle
the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to
handle
the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to
handle
the H atom.
Could someone please help me to find where I did wrong
Thanks in advance
Vittorio
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