Hi Francesco,
As I thought might be the case and mentioned in the previous mail, Amber expects protonated aspartic/glutamic acids to have the proton attached to the other oxygen.  What you need to do is simply swap the names of the oxygens in these residues and also change the '1' in the proton name to '2'.
You were right to break the long bonds, but breaking the bonds turns the formerly connected residues into terminal residues, which means you need an additional oxygen on the 'C' and two additional hydrogens on the 'N'.  In addition the hydrogen already attached to 'N' now has the wrong name, since the three hydrogens connected to an N terminus are named H1, H2, and H3, not H.  Probably the simplest way to resolve this situation is to run your structure through Dock Prep again (which will fix up the mangled terminii) and write a new PDB file.  Also, you will need to delete the unwanted N-terminal 'H' hydrogens before running Dock Prep.  You can either just delete them from your input file or use the command 'del :334,223,112,1@H'.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        pett@cgl.ucsf.edu

                        http://www.cgl.ucsf.edu



On Oct 23, 2007, at 10:33 AM, Francesco Pietra wrote:

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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