ADL: autodock Digest, Vol 56, Issue 38

corinne.portioli at virgilio.it corinne.portioli at virgilio.it
Thu Apr 23 01:10:40 PDT 2009


to answer this messagge and ask question, how can i do?

Date: Mon, 28 
Apr 2008 19:01:56 -0300 (ART)
From: "Josmar R. da Rocha" <bije_br at 
yahoo.com.br>
Subject: ADL: Warning concerning Cofactor (NAD) when 
running autogrid4
To: autodock at scripps.edu
Message-ID: <381161.46368.
qm at web55404.mail.re4.yahoo.com>
Content-Type: text/plain; 
charset=iso-8859-1


----Original Message----
From: corinne.
portioli at virgilio.it
Date: Apr 22, 2009 23:34 
To: "CORINNE PORTIOLI"
<corinne.portioli at virgilio.it>
Subj: Fw: autodock Digest, Vol 56, Issue 
38

Hi,
i would know if this problem is important or not so much in 
docking or how could i solve it.
thank you 
corinne

----- Original 
Message ----- 
From: <autodock-request at scripps.edu>
To: 
<autodock at scripps.edu>
Sent: Wednesday, April 22, 2009 8:29 PM
Subject: 
autodock Digest, Vol 56, Issue 38


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> Today's Topics:
>
>   
1. Re:  Best way to assign partial charges (??)
>   2.  New atom types 
in parameter file (Sharath Roy)
>   3.  cofactor parametrizing (corinne.
portioli at virgilio.it)
>   4.  RMSD (kannan cham)
>   5. Re:  RMSD 
(bagdevi.mishra at gmail.com)
>   6.  Error visualizing interactions 
(latha)
>   7.  Docking Software Cost (Danan S. Wicaksono)
>
>
> 
----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 Apr 2009 09:36:31 +0800 (CST)
> From: ?? 
<xuwenpku at 163.com>
> Subject: Re: ADL: Best way to assign partial 
charges
> To: autodock at scripps.edu
> Message-ID:
> <1866428.
613931240364191147.JavaMail.coremail at bj163app121.163.com>
> Content-
Type: text/plain; charset=gbk
>
> Hi,
> that's an intresting problem 
maybe you can tell everyone is that charge 
> difference make the 
docking results different after your experimental 
> docking runs.
> 
thank for sharing your experience.
>
>
>
>
> ?2009-04-21?"Douglas 
Houston" <dhouston at staffmail.ed.ac.uk> ???
>>
>>It seems that the 
Gasteiger charges calculated by prepare_ligand4.py are
>>indeed 
different from the Gasteiger charges calculated by OpenBabel.
>>
>>Most 
of them aren't that different, but some are significantly different.
>>For example, atom 5 in this molecule below is quite negatively 
charged 
>>using
>>one method, and slightly positively charged using 
the other. Since 
>>nitrogen
>>is more electronegative, it seems to me 
that it would draw electrons from
>>the carbons it's bonded to and 
would indeed have a small negative charge, 
>>so
>>it appears that, in 
this case, the OpenBabel method is more "correct"
>>(please correct me 
if I'm wrong).
>>
>>Charges added by OpenBabel 2.2.1:
>>
>>ROOT
>>ATOM      1  C   LIG d  11       0.000   0.000   0.000  0.00 
>>00    
-0.002
>>C
>>ATOM      2  C   LIG d  11      -0.595  -1.258  -0.587  
0.00 
>>00    -0.034
>>A
>>ATOM      3  C   LIG d  11       0.699  
-1.260   2.083  0.00  0.00 
>>0.065
>>C
>>ATOM      4  C   LIG d  
11       0.000   0.000   1.540  0.00  0.00 
>>0.014
>>C
>>ATOM      5  
N   LIG d  11       2.106  -1.152   1.669  0.00 
>>00    -0.295
>>N
>>ATOM      6  C   LIG d  11      -0.599  -2.453   0.142  0.00 
>>00    
-0.042
>>A
>>ATOM      7  C   LIG d  11      -0.007  -2.512   1.530  
0.00  0.00 
>>0.054
>>C
>>ATOM      8  C   LIG d  11       1.476   
0.000  -0.440  0.00  0.00 
>>0.027
>>C
>>ATOM      9  C   LIG d  
11       2.245  -1.168   0.206  0.00  0.00 
>>0.086
>>C
>>ATOM     10  
C   LIG d  11      -1.148  -1.220  -1.872  0.00  0.00 
>>0.049
>>A
>>ATOM     11  C   LIG d  11      -1.154  -3.611  -0.415  0.00  0.00 
>>0.007
>>A
>>ATOM     12  C   LIG d  11      -1.704  -2.378  -2.429  
0.00  0.00 
>>0.117
>>A
>>ATOM     13  C   LIG d  11      -0.767   
1.212  -0.522  0.00  0.00 
>>0.016
>>C
>>ATOM     14  C   LIG d  
11      -1.707  -3.573  -1.701  0.00  0.00 
>>0.045
>>A
>>ATOM     15  
C   LIG d  11      -1.433   0.067   2.061  0.00  0.00 
>>0.010
>>C
>>ENDROOT
>>BRANCH   5  16
>>ATOM     16  C   LIG d  11       2.873  
-2.267   2.244  0.00  0.00 
>>0.112
>>C
>>BRANCH  16  17
>>ATOM     17  
C   LIG d  11       3.946  -1.722   3.155  0.00 
>>00    -0.013
>>C
>>ATOM     18  C   LIG d  11       4.773  -2.562   3.793  0.00 
>>00    
-0.078
>>C
>>ATOM     19  C   LIG d  11       5.847  -2.017   4.704  
0.00  0.00 
>>0.038
>>C
>>ATOM     20  C   LIG d  11       4.631  
-4.053   3.600  0.00  0.00 
>>0.038
>>C
>>ENDBRANCH  16  17
>>ENDBRANCH   5  16
>>BRANCH  12  21
>>ATOM     21  O   LIG d  11      
-2.244  -2.341  -3.688  0.00 
>>00    -0.507
>>OA
>>ATOM     22  H   
LIG d  11      -2.242  -1.433  -4.241  0.00  0.00 
>>0.292
>>HD
>>ENDBRANCH  12  21
>>TORSDOF 3
>>
>>Charges added by prepare_ligand4.
py:
>>
>>ROOT
>>HETATM    1  C   LIG     1       0.000   0.000   0.000  
1.00 
>>00    -0.009
>>C
>>HETATM    2  C   LIG     1      -0.595  
-1.258  -0.587  1.00 
>>00    -0.040
>>A
>>HETATM    3  C   LIG     
1       0.699  -1.260   2.083  1.00  0.00 
>>0.232
>>C
>>HETATM    4  
C   LIG     1       0.000   0.000   1.540  1.00  0.00 
>>0.028
>>C
>>HETATM    5  N   LIG     1       2.106  -1.152   1.669  1.00  0.00 
>>0.097
>>N
>>HETATM    6  C   LIG     1      -0.599  -2.453   0.142  
1.00 
>>00    -0.049
>>A
>>HETATM    7  C   LIG     1      -0.007  
-2.512   1.530  1.00  0.00 
>>0.075
>>C
>>HETATM    8  C   LIG     
1       1.476   0.000  -0.440  1.00  0.00 
>>0.044
>>C
>>HETATM    9  
C   LIG     1       2.245  -1.168   0.206  1.00  0.00 
>>0.274
>>C
>>HETATM   10  C   LIG     1      -1.148  -1.220  -1.872  1.00  0.00 
>>0.045
>>A
>>HETATM   11  C   LIG     1      -1.154  -3.611  -0.415  
1.00  0.00 
>>0.010
>>A
>>HETATM   12  C   LIG     1      -1.704  
-2.378  -2.429  1.00  0.00 
>>0.066
>>A
>>HETATM   13  C   LIG     
1      -0.767   1.212  -0.522  1.00  0.00 
>>0.021
>>C
>>HETATM   14  
C   LIG     1      -1.707  -3.573  -1.701  1.00  0.00 
>>0.037
>>A
>>HETATM   15  C   LIG     1      -1.433   0.067   2.061  1.00  0.00 
>>0.013
>>C
>>ENDROOT
>>BRANCH   5  16
>>HETATM   16  C   LIG     
1       2.873  -2.267   2.244  1.00  0.00 
>>0.300
>>C
>>BRANCH  16  17
>>HETATM   17  C   LIG     1       3.946  -1.722   3.155  1.00  0.00 
>>0.005
>>C
>>HETATM   18  C   LIG     1       4.773  -2.562   3.793  
1.00 
>>00    -0.090
>>C
>>HETATM   19  C   LIG     1       5.847  
-2.017   4.704  1.00  0.00 
>>0.042
>>C
>>HETATM   20  C   LIG     
1       4.631  -4.053   3.600  1.00  0.00 
>>0.042
>>C
>>ENDBRANCH  16  
17
>>ENDBRANCH   5  16
>>BRANCH  12  21
>>HETATM   21  O   LIG     
1      -2.244  -2.341  -3.688  1.00 
>>00    -0.361
>>OA
>>HETATM   22  
H   LIG     1      -2.242  -1.433  -4.241  1.00  0.00 
>>0.217
>>HD
>>ENDBRANCH  12  21
>>TORSDOF 3
>>
>>I plan to re-dock a large number 
of molecules using the new charges and 
>>see
>>if they make a big 
difference to the rankings.
>>-- 
>>View this message in context: 
>>http://n2.nabble.com/Best-way-to-assign-partial-charges-
tp2642998p2669536.html
>>Sent from the AutoDock mailing list archive at 
Nabble.com.
>>
>>________________________________________________
>>--- 
ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 22 Apr 
2009 11:33:42 +0530 (IST)
> From: Sharath Roy <royshari87 at yahoo.in>
> 
Subject: ADL: New atom types in parameter file
> To: autodock at scripps.
edu
> Message-ID: <14889.79129.qm at web95104.mail.in2.yahoo.com>
> 
Content-Type: text/plain; charset=utf-8
>
> Hi ..........
>
> In a 
docking program, I found the dlg not to be found for certain entries 
> 
because of having extra atom types in ligand-pdbqt......the extra 
types 
> are As, Cu, Sb and so on.........
> So, this has to be added 
in the AD4_parameters.dat..........
>
> My question is we shud also 
provide with the Rii , solpar, rec_index 
> etc..........parameters 
...........So hw is this accomplished???
>
> When I use the 
prepare_ligand4.py script for preparing the lig, it shows a 
> warning 
so as to Gastegier charges cannot be computed for the extra atom 
> 
types..........But i did it in ADT, and it assigned zero charge for 
those 
> extra atoms............
>
> But it s taken into problematic 
consideration in autodock -step..........
>
> How to proceed??
>
> 
Thanx in advance
>
>
>
>      Now surf faster and smarter ! Check out 
the new Firefox 3 - Yahoo! 
> Edition http://downloads.yahoo.
com/in/firefox/
>
> ------------------------------
>
> Message: 3
> 
Date: Wed, 22 Apr 2009 11:24:21 +0100 (GMT+01:00)
> From: "corinne.
portioli at virgilio.it" <corinne.portioli at virgilio.it>
> Subject: ADL: 
cofactor parametrizing
> To: autodock at scripps.edu
> Message-ID: 
<120cd5acfac.corinne.portioli at virgilio.it>
> Content-Type: text/plain;
charset="UTF-8"
>
> good morning,
>
> i`m working with autodock4. 
during the preparation of my
> protein that present a cofactor NADP+ 
insite. i read from the file gpf
> to glg this message:  `WARNING:  
Oxygen atom found with no bonded
> atoms, atom serial number 3123, 
atom_type 5` for all oxygen atoms that
> have all OA that will be 
correct. also with this message i can go on my
> wotk. so
> i would 
know if there some way to parametrizing cofactor or if
> this message 
is of high or low importance.
> waiting an answer
> i thank
> you
> 
best regards
> Corinne
>
>
> ------------------------------
>
> 
Message: 4
> Date: Wed, 22 Apr 2009 15:56:37 +0530 (IST)
> From: kannan 
cham <kannan_cmn at yahoo.co.in>
> Subject: ADL: RMSD
> To: 
autodock at scripps.edu
> Message-ID: <659940.82138.qm at web8608.mail.in.
yahoo.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi
>
> Can 
anyone tell me how to find the RMSD after the docking.... and also
> 
tell me what is the range of the RMSD values....Thank you..
>
>
>
>
>
>
>
>      Now surf faster and smarter ! Check out the new Firefox 3 - 
Yahoo! 
> Edition http://downloads.yahoo.com/in/firefox/
>
> 
------------------------------
>
> Message: 5
> Date: Wed, 22 Apr 2009 
17:33:39 +0530
> From: bagdevi.mishra at gmail.com
> Subject: Re: ADL: 
RMSD
> To: autodock at scripps.edu
> Message-ID:
> 
<c1a055830904220503m1e92e37dq46bc6c0429cbd1a0 at mail.gmail.com>
> Content-
Type: text/plain; charset=ISO-8859-1
>
> after getting the dlg file you 
can run the python code 
> summarize_results4.py
>
>
> It has following 
options.
>
> Usage: summarize_results4.py -d directory
>
>    
Description of command...
>         -d     directory
>    Optional 
parameters:
>        [-t]    rmsd tolerance (default is 1.0)
>        [-
f]    rmsd reference filename
>        (default is to use input ligand 
coordinates from docking log)
>        [-b]    print best docking info 
only (default is print all)
>        [-L]    print largest cluster info 
only (default is print all)
>        [-B]    print best docking and 
largest cluster info only (default 
> is
> print all)
>        [-o]    
output filename
>                      (default is 
'summary_of_results')
>        [-a]    append to  output filename
>                      (default is to open output filename 'w')
>        [-k]    build hydrogen bonds and report number built
>        
[-e]    compute estat, vdw, hb + desolv energies and report
> breakdown
>        [-r]    receptor filename
>        [-u]    report unbound 
energy
>        [-i]    subtract internal energy
>        [-p]    
report depth of torsion tree
>        [-v]    verbose output
>
>
>
>
> 
On Wed, Apr 22, 2009 at 3:56 PM, kannan cham <kannan_cmn at yahoo.co.in> 
> wrote:
>
>> Hi
>>
>> Can anyone tell me how to find the RMSD after 
the docking.... and also
>> tell me what is the range of the RMSD 
values....Thank you..
>>
>>
>>
>>
>>
>>
>>
>>      Now surf faster and 
smarter ! Check out the new Firefox 3 - Yahoo!
>> Edition http:
//downloads.yahoo.com/in/firefox/
>> 
________________________________________________
>> --- ADL: AutoDock 
List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
> 
------------------------------
>
> Message: 6
> Date: Wed, 22 Apr 2009 
11:21:43 -0500
> From: latha <latha.9999 at gmail.com>
> Subject: ADL: 
Error visualizing interactions
> To: autodock at scripps.edu
> Message-ID:
> <16e2ee070904220921r3140209di48460211f88a2ca at mail.gmail.com>
> 
Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
>            I 
am trying to visualize interactions using the .dlg file and
> the .
pdbqt file.  I tried both ADT1.5.2 and 1.5.4 versions by choosing
> AD4.
1. I have used autodock4 for docking. I searched archives, but I 
> 
didn't
> find much help. I am posting for the second time.
>
> I  am 
getting the following error
>
>>>> ERROR 
*********************************************
> Traceback (most recent 
call last):
>  File "C:\Program Files\MGLTools
> 1.5.2
\MGLToolsPckgs\ViewerFramework\VF.py", line 716, in tryto
>    result = 
apply( command, args, kw )
>  File "C:\Program Files\MGLTools
> 1.5.2
\MGLToolsPckgs\AutoDockTools\autoanalyzeCommands.py", line 2087, in
> 
doit
>    self.build()
>  File "C:\Program Files\MGLTools
> 1.5.2
\MGLToolsPckgs\AutoDockTools\autoanalyzeCommands.py", line 1912, in
> 
build
>    self.intDescr = InteractionDescriptor(lig, macro, 
percentCutoff)
>  File "C:\Program Files\MGLTools
> 1.5.2
\MGLToolsPckgs\MolKit\interactionDescriptor.py", line 46, in __init__
>    self.build(detect_pi=detect_pi)
>  File "C:\Program Files\MGLTools
> 1.5.2\MGLToolsPckgs\MolKit\interactionDescriptor.py", line 56, in 
build
>    self.buildCloseContactAtoms(percentCutoff)              #
>  
File "C:\Program Files\MGLTools
> 1.5.2
\MGLToolsPckgs\MolKit\interactionDescriptor.py", line 65, in
> 
buildCloseContactAtoms
>    self.macro_atoms, 
percentCutoff=percentCutoff)
>  File "C:\Program Files\MGLTools
> 1.5.2
\MGLToolsPckgs\MolKit\distanceSelector.py", line 106, in select
>    
bigC = Numeric.resize(c, (lenC, lenC, 3))
>  File "C:\Program 
Files\MGLTools
> 1.5.2\MGLToolsPckgs\numpy\core\fromnumeric.py", line 
541, in resize
>    a = concatenate( (a,)*n_copies)
> MemoryError
>
> 
Orelse is there any other software, I can use for this purpose? Any 
kind 
> of
> help in this regard is highly appreciable.
>
> Thanks and 
regards,
> Latha,
> Graduate student.
>
>
> 
------------------------------
>
> Message: 7
> Date: Wed, 22 Apr 2009 
14:29:40 -0400 (EDT)
> From: "Danan S. Wicaksono" <danan at cmu.edu>
> 
Subject: ADL: Docking Software Cost
> To: autodock at scripps.edu
> 
Message-ID: <1680.24.3.18.241.1240424980.squirrel at 24.3.18.241>
> 
Content-Type: text/plain;charset=iso-8859-1
>
> Dear Docking Software 
Users,
>
> Would you please share with me the costs for academic 
licenses of some of 
> the docking softwares below:
>
> GOLD
>
> FlexX
>
> Gold
>
> ICM
>
> Your help is truly appreciated.
>
> Regards,
>
> 
Danan
>
>
>
> ------------------------------
>
> 
________________________________________________
> --- ADL: AutoDock 
List  ---  
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 56, Issue 38
> 
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