Hi Francesco,
I haven't used the capActiveSite executable myself, but I guess that the "ligand file" is not simply the metalloprotein with the metal taken out (i.e., the apo state). Instead, the ligand file would be a PDB or mol file containing only the ligand that binds to the metal+protein assembly. I'm not even sure if water would count as a "ligand" for these purposes, though it may. Martin, can you advise here, even if just for the benefit of the list archives?
For MCPB, examples of script files (also called bcl scripts and other names) can be found in subsection 15.10 of the MTK++ manual (named MTKpp.pdf). I would encourage you to focus specifically on subsections 15.10.4 (the settings file), 15.10.6 (the side chain model) and 15.10.9 (the large model). The monospaced text in 15.10.6 and 15.10.9 is the contents of example script files. Please note that because they are examples, you may need to change some things, rather than simply copying what's there verbatim.
I hope that helps. Feel free to email the list if you have further questions.
Cheers,
Ben
On 24/09/2012, at 9:40 PM, Francesco Pietra wrote:
> Ben:
> In order to better illustrate what I did, I used the indications at
>
> Modeling ToolKit++ (MTK++)
> v0.2.0
> April 2010
> Last revised, March 2011
>
>
> 15.1
> Active Site Capping (capActiveSite)
> Given a co-crystallized PDB file this utility can cut out the active
> site and cap the resulting amino
> acid strands.
> The program has the following options:
> capActiveSite: Caps active site using a cutoff
> usage: capActiveSite [flags] [options]
> options:
> -r receptor pdb file
> -l ligand mol/pdb file
> -c distance cutoff [10.0]
> -o output pdb file
> -a log file
>
>
> As I already said, submitting the metalloprotein alone, the code asked
> for the ligand pdb file. I did that by removing the metal and its
> HO/H2O, taking this as the ligand pdb file (while I was much in
> doubt).
> .......................
>
> I was aware about the Ambertools12 (which I used) manual indications
>
> 4.6.2. Running MCPB
> MCPB takes two command-line arguments. One is the control file, which
> is required and
> chosen with the -i flag. The other is the log file, which is optional
> and chosen with the -l flag.
> A full listing of all the commands used by MCPB can be obtained with
> the -f flag.
> MCPB: Semi-automated tool for metalloprotein parametrization
> usage: MCPB [flags] [options]
> options:
> -i script file
> -l log file
> flags:
> -h help
> -f function list
> Full details of a metalloprotein parametrization procedure using MCPB
> can be found in section
> 15.10 of the user manual. This example describes the active site
> parametrization of a di-zinc
> system (PDB ID: 1AMP). The parametrization is broken down into stages
> since several MCPB ....
> ..................
>
> I first tried to follow this route but I was unable to find an example
> of the "script file", nor the files mentioned in the MTK manual
> (except the input pdb in folder /tests).
>
> I hope now to have clarified what I did.
>
> thanks for your kind attention.
> francesco
>
>
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret.gmail.com>
> Date: Mon, Sep 24, 2012 at 8:47 AM
> Subject: Re: [AMBER] MTK++ Error: no active site found
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> On Mon, Sep 24, 2012 at 6:43 AM, Ben Roberts <ben.roberts.geek.nz> wrote:
>> Hi Francesco,
>>
>> I understand. I'll look into it a bit further.
>
> Hello Ben:
> Thanks for your promised help.
>
> I have already parameterized several transition-metal centers of
> metalloproteins, either parm7 of charmm27, "by hand". I wanted to see
> if the MCPB tool can speed up the process, although I was perplexed
> about the lack - in places - of searching a stationary point. I'll go
> further "by hand" as before, while I hope to be put on the right way
> to understand MCPB. I suspect I have misunderstood the start.
>
> The exchange will be slow: New Zealand (which I hope one day to visit,
> so far new Caledonia was the nearest I visited) lies at nearly the
> opposite side of Central Europe.
>
> francesco
>>
>> 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
>
> _______________________________________________
> 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
Received on Tue Sep 25 2012 - 17:30:03 PDT
