[Chimera-users] Atom does not have a type

Tue Oct 23 10:33:49 PDT 2007

Thanks to Eric Pettersen I have fixed problems of long bonds and
mis-assignement by prepare_amber.pl  (from HIS to HIE, while it is HID).

Two types of problems remain because I was either unable to correct or did
wrongly. The error log from attempted fixing problems:
WARNING: The unperturbed charge of the unit: 24.000000 is not zero.
FATAL:  Atom .R<GLH 443>.A<HE1 17> does not have a type.
FATAL:  Atom .R<ASH 402>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 386>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 375>.A<HD1 14> does not have a type.
FATAL:  Atom .R<GLH 373>.A<HE1 17> does not have a type.
FATAL:  Atom .R<NSER 334>.A<H 14> does not have a type.
FATAL:  Atom .R<GLH 332>.A<HE1 17> does not have a type.
FATAL:  Atom .R<ASH 291>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 275>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 264>.A<HD1 14> does not have a type.
FATAL:  Atom .R<GLH 262>.A<HE1 17> does not have a type.
FATAL:  Atom .R<NSER 223>.A<H 14> does not have a type.
FATAL:  Atom .R<GLH 221>.A<HE1 17> does not have a type.
FATAL:  Atom .R<ASH 180>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 164>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 153>.A<HD1 14> does not have a type.
FATAL:  Atom .R<GLH 151>.A<HE1 17> does not have a type.
FATAL:  Atom .R<GLH 128>.A<HE1 17> does not have a type.
FATAL:  Atom .R<NSER 112>.A<H 14> does not have a type.
FATAL:  Atom .R<GLH 110>.A<HE1 17> does not have a type.
FATAL:  Atom .R<ASH 69>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 53>.A<HD1 14> does not have a type.
FATAL:  Atom .R<ASH 42>.A<HD1 14> does not have a type.
FATAL:  Atom .R<GLH 40>.A<HE1 17> does not have a type.
FATAL:  Atom .R<GLH 17>.A<HE1 17> does not have a type.
FATAL:  Atom .R<NSER 1>.A<H 14> does not have a type.

UNABLE : I don't know how to rename the hydrogen on serine nitrogen. In my
protein.pdb, the section around residues 333/334:

ATOM   5155  O   THR X 333      15.694 -15.150  25.132  0.00  0.00           O
TER    5156      THR X 333
ATOM   5157  N   SER X 334     -16.176  22.312  10.940  0.00  0.00           N
ATOM   5158  H   SER X 334     -15.301  22.760  10.966  0.00  0.00           H
ATOM   5159  CA  SER X 334     -16.224  20.932  11.429  0.00  0.00           C
ATOM   5160  HA  SER X 334     -17.198  20.770  11.905  0.00  0.00           H
ATOM   5161  CB  SER X 334     -15.868  19.959  10.306  0.00  0.00           C
ATOM   5162  HB2 SER X 334     -15.761  18.918  10.709  0.00  0.00           H
ATOM   5163  HB3 SER X 334     -14.903  20.280   9.956  0.00  0.00           H
ATOM   5164  OG  SER X 334     -16.906  19.973   9.300  0.00  0.00           O
ATOM   5165  HG  SER X 334     -16.948  20.844   8.983  0.00  0.00           H
ATOM   5166  C   SER X 334     -15.185  20.856  12.533  0.00  0.00           C
ATOM   5167  O   SER X 334     -14.212  21.643  12.566  0.00  0.00           O

Actually, I only inserted "TER" (where it is now) between residue 333 and 334
to get rid of a long bond between the two; numbering and THR X 333 came out
automatically. Also, automatically the pdb file now begins with a series of
HELIX.

BADLY DONE: to correct for the carboxyl hydrogen being on the wrong oxygen of
ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the section

ATOM   6851  CD  GLU X 443     -10.347  20.009  21.724  0.00  0.00            
ATOM   6852  OE1 GLU X 443     -10.341  20.227  23.079  0.00  0.00            
ATOM   6853  OE2 GLU X 443     -10.192  20.919  20.907  0.00  0.00            
ATOM   6854  HE1 GLU X 443     -10.239  21.145  23.232  0.00  0.00

was rewritten by exchanging two lines, which automatically were renumbered

ATOM   6854  CD  GLH X 443     -10.347  20.009  21.724  0.00  0.00           C
ATOM   6855  OE1 GLH X 443     -10.341  20.227  23.079  0.00  0.00           O
ATOM   6856  OE2 GLH X 443     -10.192  20.919  20.907  0.00  0.00           O
ATOM   6857  HE1 GLH X 443     -10.239  21.145  23.232  0.00  0.00           H
ATOM   6858  C   GLH X 443     -13.205  16.911  22.895  0.00  0.00           C

and the issue on prepare_amber.pl was not resolved.

It is obvious that I am carrying out such adjustments for the first time. I got
the impression that from now on, what I do increases the mess.

Must say that with my imperfect pdb I could carry outt all DOCK tutorials,
except the amber_score.

Thanks
francesco pietra

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