psfgen and charmm19: is there any inconsistency?

From: Magali Cottevieille (magali.cottevieille_at_impmc.jussieu.fr)
Date: Tue Jun 27 2006 - 03:18:20 CDT

Hi everybody,

I have serious error messages when I try to use psfgen with toph19.inp,
cf. below (atoms seems to be missing whereas they do exist, specifically
for residues phe, trp and tyr).
Can anyboldy help me? I am a new user of psfgen and namd. Of course I
have checked I had the same definitions of atoms between my pdb file and
the topology file (besides, it doesn't come from the pdb file, it does
the same with several other ones). Do you think it comes from
toph19.inp? Because there is no problem if I use
top_all27_prot_lipid.inp, as in namd tutorial...

Thanks a lot,
Magali.

----
Output of psfgen run on ubiquitin with toph19.inp:
Created by CHARMM version 21 1
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
ERROR!  Explicit exclusions or fluctuating charges not supported, atom 
ignored.
aliasing residue ILE atom CD1 to CD
building segment U
reading residues from pdb file ubqp.pdb
extracted 76 residues from pdb file
Info: generating structure...
no residue 1 before MET:1 of segment U
Warning: add dihedral failed in residue MET:1
Info: skipping improper N-C-CA-H at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-H at beginning of segment.
ERROR: Missing atoms for bond CD2(0) CE2(0) in residue PHE:4
ERROR: Missing atoms for bond CD1(0) CE1(0) in residue PHE:4
ERROR: Missing atoms for bond CG(0) CD2(0) in residue PHE:4
ERROR: Missing atoms for bond CG(0) CD1(0) in residue PHE:4
ERROR: Missing atoms for bond CB(0) CG(0) in residue PHE:4
no atom CG in residue PHE:4 of segment U
Warning: add dihedral failed in residue PHE:4
no atom CG in residue PHE:4 of segment U
Warning: add dihedral failed in residue PHE:4
ERROR: Missing atoms for improper CG(0) CD1(0) CD2(0) CB(0)
    in residue PHE:4
ERROR: Missing atoms for improper CD2(0) CG(0) CD1(0) CE1(0)
    in residue PHE:4
ERROR: Missing atoms for improper CE2(0) CD2(0) CG(0) CD1(0)
    in residue PHE:4
ERROR: Missing atoms for improper CZ(0) CE2(0) CD2(0) CG(0)
    in residue PHE:4
ERROR: Missing atoms for improper CE1(0) CZ(0) CE2(0) CD2(0)
    in residue PHE:4
ERROR: Missing atoms for improper CD1(0) CE1(0) CZ(0) CE2(0)
    in residue PHE:4
ERROR: Missing atoms for improper CG(0) CD1(0) CE1(0) CZ(0)
    in residue PHE:4
ERROR: Missing atoms for bond CD2(0) CE2(0) in residue PHE:45
ERROR: Missing atoms for bond CD1(0) CE1(0) in residue PHE:45
ERROR: Missing atoms for bond CG(0) CD2(0) in residue PHE:45
ERROR: Missing atoms for bond CG(0) CD1(0) in residue PHE:45
ERROR: Missing atoms for bond CB(0) CG(0) in residue PHE:45
no atom CG in residue PHE:45 of segment U
Warning: add dihedral failed in residue PHE:45
no atom CG in residue PHE:45 of segment U
Warning: add dihedral failed in residue PHE:45
ERROR: Missing atoms for improper CG(0) CD1(0) CD2(0) CB(0)
    in residue PHE:45
ERROR: Missing atoms for improper CD2(0) CG(0) CD1(0) CE1(0)
    in residue PHE:45
ERROR: Missing atoms for improper CE2(0) CD2(0) CG(0) CD1(0)
    in residue PHE:45
ERROR: Missing atoms for improper CZ(0) CE2(0) CD2(0) CG(0)
    in residue PHE:45
ERROR: Missing atoms for improper CE1(0) CZ(0) CE2(0) CD2(0)
    in residue PHE:45
ERROR: Missing atoms for improper CD1(0) CE1(0) CZ(0) CE2(0)
    in residue PHE:45
ERROR: Missing atoms for improper CG(0) CD1(0) CE1(0) CZ(0)
    in residue PHE:45
ERROR: Missing atoms for bond CE1(0) CZ(0) in residue TYR:59
ERROR: Missing atoms for bond CD1(0) CE1(0) in residue TYR:59
ERROR: Missing atoms for bond CG(0) CD2(0) in residue TYR:59
ERROR: Missing atoms for bond CG(0) CD1(0) in residue TYR:59
ERROR: Missing atoms for bond CB(0) CG(0) in residue TYR:59
no atom CG in residue TYR:59 of segment U
Warning: add dihedral failed in residue TYR:59
no atom CG in residue TYR:59 of segment U
Warning: add dihedral failed in residue TYR:59
ERROR: Missing atoms for improper CD2(0) CG(0) CD1(0) CE1(0)
    in residue TYR:59
ERROR: Missing atoms for improper CE2(0) CD2(0) CG(0) CD1(0)
    in residue TYR:59
ERROR: Missing atoms for improper CZ(0) CE2(0) CD2(0) CG(0)
    in residue TYR:59
ERROR: Missing atoms for improper CE1(0) CZ(0) CE2(0) CD2(0)
    in residue TYR:59
ERROR: Missing atoms for improper CD1(0) CE1(0) CZ(0) CE2(0)
    in residue TYR:59
ERROR: Missing atoms for improper CG(0) CD1(0) CE1(0) CZ(0)
    in residue TYR:59
ERROR: Missing atoms for improper CZ(0) CE1(0) CE2(0) OH(0)
    in residue TYR:59
ERROR: Missing atoms for improper CG(0) CD1(0) CD2(0) CB(0)
    in residue TYR:59
Info: skipping bond C-N at end of segment.
no residue 1 past GLY:76 of segment U
Warning: add dihedral failed in residue GLY:76
no residue 1 past GLY:76 of segment U
Warning: add dihedral failed in residue GLY:76
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
reading coordinates from pdb file ubqp.pdb for segment U
Warning: failed to set coordinate for atom CG     PHE:4      U
Warning: failed to set coordinate for atom CD1     PHE:4      U
Warning: failed to set coordinate for atom CD2     PHE:4      U
Warning: failed to set coordinate for atom CG     PHE:45      U
Warning: failed to set coordinate for atom CD1     PHE:45      U
Warning: failed to set coordinate for atom CD2     PHE:45      U
Warning: failed to set coordinate for atom CG     TYR:59      U
Warning: failed to set coordinate for atom CD1     TYR:59      U
Warning: failed to set coordinate for atom CE1     TYR:59      U
Warning: failed to set coordinate for atom O     GLY:76      U
Warning: failed to set coordinate for atom OXT     GLY:76      U
Info: guessing coordinates for 146 atoms (2 non-hydrogen)
...
-- 
Magali COTTEVIEILLE, Département de Biologie Structurale
I.M.P.M.C., UMR CNRS 7590, Univ. P. et M. Curie
140 Rue de Lourmel, 75015 Paris
Tel +33 (0)144 27 52 41  Fax +33 (0)144 27 37 85
E-mail : magali.cottevieille_at_impmc.jussieu.fr
URL : http://www.lmcp.jussieu.fr/~cottevie/

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