Dear Sir,

I have mentioned here few warnings, not errors, but as they affect final model, I need to handle them, please explain the reasons behind them and method to remove them. Although, necessary changes I have tried to make in all possible files and I have mentioned about them here. Sorry, its a bit lengthy mail, but plz spare out some time frm your schedule to explain these.

PS: I have added residues to top_heav.lib and using my own par.lib which also includes all required parameters for new residues added in top_heav.lib (may be some few are missing).

1. I have included few new residue types in top_heav.lib and made necessary changes in res_type.lib also, but still it gives the statement

> Non-standard residue type,position,sequence: / 655 1 > Non-standard residue type,position,sequence: + 656 1 > Non-standard residue type,position,sequence: + 657 1

like this, although its not a warning, but why this is so? and where the change is needed to be made?

2. This is warning, is it serious enough or not and how to remove this?

fndatmi_285W> Number of residues <> number of atoms; atom code: 516 513 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 541 538 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 547 544 CA

3. Are these atoms for which no coordinates are defined, the undefined ones? meaning there by that these types are either not present in top_heav.lib or par.lib . So how to handle this or MODELER itself is handling it.

build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates.

4. Serious one: I have used my own par.lib not the one which is supplied with MODELER, and it shows the following warnings , I think this means that there are no parameters available for these dihedrals and MODELER is assigning the values by some means (random generation). So, if I am able to get the values of dihedrals, then by putting the values in my par.lib, these warnings can be removed, am I right? And if I dont found these values anywhere, then to what level these MODELER generated values are acceptable?

r_stere_607W> Cannot find params in params file: CHARMM atoms : CT1 NH3 C CT2 IUPAC atoms : CA N C CB Atom indices : 2 1 7 3 Residues : MET MET MET MET addprm__440W> Adding params (mean,force,period): 33.6945 60.0000 0 For atoms: CT1 NH3 C CT2 r_stere_607W> Cannot find params in params file: CHARMM atoms : CT1 NH1 C CT2 IUPAC atoms : CA N C CB Atom indices : 10 9 15 11 Residues : LEU LEU LEU LEU addprm__440W> Adding params (mean,force,period): 33.6297 60.0000 0 For atoms: CT1 NH1 C CT2 r_stere_607W> Cannot find params in params file: CHARMM atoms : CT1 CT3 CT3 CT2 IUPAC atoms : CG CD1 CD2 CB Atom indices : 12 13 14 11 Residues : LEU LEU LEU LEU addprm__440W> Adding params (mean,force,period): 32.3756 60.0000 0

5. While restraints making , it shows the following warnings, i dont understand these, please explain.

make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 512 LEU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 513 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 513 LYS

6. this also , I hope to be a serious one. Although , topology file includes the residues with same details as in pdb, i.e. same PDB atom names, all specific CHARMM atom names, etc. but what does this warning signify,please explain.

make_re_417_> Restraint type to be calculated: distance iup2crm_279W> IUPAC atom not found in topology library; residue type index: N A 143 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom not found in topology library; residue type index: N B 143 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom not found in topology library; residue type index: N C 143 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library.

These are 6 questions, please explain the possible cures for these.

Thanks in advance,

sincerely,

vivek sharma