Hi Francesco,
I understand. I'll look into it a bit further.
Cheers,
Ben
On 24/09/2012, at 10:19 AM, Francesco Pietra wrote:
> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
For greater security, I support S/MIME encryption.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 23 2012 - 22:00:03 PDT
