Hello:
I am using MCPB in AmberTools12 for the first time, trying to
parameterize the active site of an iron protein.
I was unable to find the specific files mentioned in the examples of
the MTK++ manual. Therefore, what I did, was to provide two files, one
for the receptor protein (resid re-numbered from one) and the other
one for the two iron atoms and OH and H2O bound to them (resid
numbered as in the original PDB from X-ray diffr).
COMMAND capActiveSite -r protein.pdb -l Fe_OH_H2O.pdb -c [5] -o
capped.pdb -a capped.log
Selected parts of the log file follow:
### ### ### ###
### MTK++ Warning ###
### Function: pdbParser ###
### Message: Can't determine 1-letter code for FE . Using 'X'.
### ### ### ###
### ### ### ###
### MTK++ Warning ###
### Function: pdbParser ###
### Message: Can't determine 1-letter code for FE . Using 'X'.
### ### ### ###
..........................
..........................
### ### ### ###
### MTK++ Warning ###
### Function: atomTyper::atomTypeByLib ###
### Message: Unable to assign stdFrag: unknown residue |FE |
### ### ### ###
### ### ### ###
### MTK++ Warning ###
### Function: atomTyper::atomTypeByLib ###
### Message: Unable to assign stdFrag: unknown residue |FE |
### ### ### ###
............................
............................
### ### ### ###
### MTK++ Info ###
### Function: connections::assignStdBonds ###
### Message: Molecule # 2
Unable to assign parameters for bond : FE - O
Unable to assign parameters for bond : FE - O
Unable to assign parameters for bond : FE - O
Unable to assign parameters for bond : FE - O
Total Number of Missing Bond Parameters = 4
### ### ### ###
................................
### ### ### ###
### MTK++ Info ###
### Function: connections::assignStdAngles ###
### Message:
Unable to assign parameters for angle: FE - O - H2
Unable to assign parameters for angle: FE - O -FE
Unable to assign parameters for angle: FE - O - H1
Unable to assign parameters for angle: FE - O - H2
Unable to assign parameters for angle: O -FE - O
Unable to assign parameters for angle: O -FE - O
Unable to assign parameters for angle: H2 - O -FE
Unable to assign parameters for angle: FE - O - H1
Total Number of Missing Angle Parameters = 8
.........................................
### ### ### ###
### MTK++ Info ###
### Function: collection::hasMetal ###
### Message:
Found Metal: Fe
### ### ### ###
### ### ### ###
### MTK++ Info ###
### Function: collection::findMetals ###
### Message:
Metal Found:
Fe:1
Fe:4
### ### ### ###
...........................................
## ### ### ###
### MTK++ Info ###
### Function: collection::assignMetalParameters ###
### Message:
Metal Center: 1
Adding Primary Bonds:
FE .|FE |-GLU103 .| OE1| dist = 2.00129
FE .|FE |-GLU133 .| OE1| dist = 2.00485
FE .|FE |-HIE136 .| ND1| dist = 2.3015
FE .|FE |-HOH493 .| O | dist = 1.96646
FE .|FE |-HOH496 .| O | dist = 2.09886
GLU.| OE1|-FE .|FE |-GLU.| OE1| angle = 88.8489
GLU.| OE1|-FE .|FE |-HIE.| ND1| angle = 102.155
GLU.| OE1|-FE .|FE |-HOH.| O | angle = 165.507
GLU.| OE1|-FE .|FE |-HOH.| O | angle = 86.2372
FE .| OE1|-GLU.| OE1|-GLU.| CD | angle = 138.979
GLU.| OE1|-FE .|FE |-HIE.| ND1| angle = 93.7331
GLU.| OE1|-FE .|FE |-HOH.| O | angle = 94.5608
GLU.| OE1|-FE .|FE |-HOH.| O | angle = 172.64
FE .| OE1|-GLU.| OE1|-GLU.| CD | angle = 136.289
HIE.| ND1|-FE .|FE |-HOH.| O | angle = 91.6925
HIE.| ND1|-FE .|FE |-HOH.| O | angle = 92.6571
FE .| ND1|-HIE.| ND1|-HIE.| CG | angle = 126.844
FE .| ND1|-HIE.| ND1|-HIE.| CE1| angle = 123.676
Metal Center: 2
Adding Primary Bonds:
FE .|FE |-GLU133 .| OE2| dist = 2.14501
FE .|FE |-GLU196 .| OE2| dist = 2.0191
FE .|FE |-GLU230 .| OE2| dist = 2.20426
FE .|FE |-HID233 .| NE2| dist = 2.23017
FE .|FE |-HOH493 .| O | dist = 1.9303
FE .|FE |-HOH495 .| O | dist = 2.17406
GLU.| OE2|-FE .|FE |-GLU.| OE2| angle = 80.6702
GLU.| OE2|-FE .|FE |-GLU.| OE2| angle = 168.099
GLU.| OE2|-FE .|FE |-HID.| NE2| angle = 86.0885
GLU.| OE2|-FE .|FE |-HOH.| O | angle = 99.4688
GLU.| OE2|-FE .|FE |-HOH.| O | angle = 85.0657
FE .| OE2|-GLU.| OE2|-GLU.| CD | angle = 126.697
GLU.| OE2|-FE .|FE |-GLU.| OE2| angle = 91.8473
GLU.| OE2|-FE .|FE |-HID.| NE2| angle = 100.209
GLU.| OE2|-FE .|FE |-HOH.| O | angle = 165.773
GLU.| OE2|-FE .|FE |-HOH.| O | angle = 86.5822
FE .| OE2|-GLU.| OE2|-GLU.| CD | angle = 131.359
GLU.| OE2|-FE .|FE |-HID.| NE2| angle = 86.1545
GLU.| OE2|-FE .|FE |-HOH.| O | angle = 90.0625
GLU.| OE2|-FE .|FE |-HOH.| O | angle = 103.832
FE .| OE2|-GLU.| OE2|-GLU.| CD | angle = 124.965
HID.| NE2|-FE .|FE |-HOH.| O | angle = 93.9839
HID.| NE2|-FE .|FE |-HOH.| O | angle = 167.832
FE .| NE2|-HID.| NE2|-HID.| CD2| angle = 120.744
FE .| NE2|-HID.| NE2|-HID.| CE1| angle = 128.722
number of metal atoms = 2
number of metal centers = 2
number of metal groups = 1
### ### ### ###
..........................
### ### ### ###
### MTK++ Info ###
### Function: capActiveSite ###
### Message: Get all residues not in the ligand
### ### ### ###
### ### ### ###
### MTK++ Error ###
### Function: capActiveSite ###
### Message: No active site found
### ### ### ###
END OF LOG FILE
I am not sure what that means: (a) incorrect protein pdb; (b)
incorrect name "FE" for iron; (c) MCPB can not handle iron.
Thanks for advice
francesco pietra
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Received on Sun Sep 23 2012 - 03:30:03 PDT
