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
--
VIVEK SHARMA
HBG BI