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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