On Sun, Sep 23, 2012 at 11:24 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Francesco,
>
> Could you please post the BCL script that's giving you grief?
Ben
Sorry, I don't understand "BCL script". I just used the command that I
posted. And I was strongly in doubt whether the metal with its water
and OH is what in the manual is intended for "ligand".
francesco
francesco
>
> 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 - 15:30:02 PDT
