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
>>>>
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>>>
>>>
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Received on Mon Sep 24 2012 - 03:00:02 PDT
