Hi Francesco,
Could you please post the BCL script that's giving you grief?
Cheers,
Ben
On 23/09/2012, at 10:08 PM, Francesco Pietra wrote:
> 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 - 14:30:02 PDT
