[Dock-fans] Distorted bond Angles

Trent E. Balius tbalius at aol.com
Mon Jun 20 09:52:18 PDT 2011


Hi Marco, 


Try changing flex.defn

from:

> name           aromatic-aromatic
> driver_id      3
> minimize       0

to:

< name          aromatic-aromatic
< drive_id      3
< minimize      0

See if this resolves the problem. 

However, dock needs better error cheeking in this part of the source code (reading in flex.defn).

Really, dock should exit with an error. 

32649  dihedrals probably has to do with assigning max int or (-1) which should not occur and may be a bug. 


 I hope this helps,

 

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Marco <marco at chimfarm.unipg.it>
To: tbalius at aol.com
Sent: Mon, Jun 20, 2011 11:18 am
Subject: Re: [Dock-fans] Distorted bond Angles


Hi Trent.
Thank you for your patience. 
Here you have the files I'm using to dock my compound.
Just I said to you before, using the rigid protocol of the generated
compounds I obtain results very near to the experimental data I have. For
this reason it would be wonderful taking into account for flexibility in one
step using the flex capabilities of dock6.4.
Thank you again, 
Marco 

----
Marco Cellanetti, 
PhD Student.
Bachelor Degree in Medicinal Chemistry and Technology of Drugs

University of Perugia
Department of Medicinal Chemistry and Drug's Technology
Via del Liceo, 1 - 06123 Perugia (Italy)
Tel ++39 075 585 5169/5114



--------- Messaggio Originale --------
Da: Trent E. Balius <tbalius at aol.com>
Per: marco at chimfarm.unipg.it <marco at chimfarm.unipg.it>
Oggetto: Re: [Dock-fans] Distorted bond Angles
Data: 20/06/11 13:57

> 
> Hi Marco,
> 
> You should not be getting so many dihedral angles sampled.  The
number of dihedrals range from 0 - 8 angles.  These angles are defined
in  flex_defn.tbl
> 
> Perhaps, there is something wrong with the format of your flex.defn or
flex_defn.tbl files.
> 
> If you want you can e-mail me your flex.defn, flex_defn.tbl and mol2 files
and I can take a look.
> 
> Good luck,
> 
> Trent 
> 
> 
>  
> 
> 
> 
> 
> 
> -----Original Message-----
> 
> From: Marco <marco at chimfarm.unipg.it>
> 
> To: tbalius at aol.com
> 
> Sent: Mon, Jun 20, 2011 5:20 am
> 
> Subject: Re: [Dock-fans] Distorted bond Angles
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Hi Trent, 
> with your "aromatic-aromatic" definition I can sample the bond between the
> rings of the biphenyl system. But due to the huge number of dihedrals
(more
> than 32000) I got a segmentation fault.
> I'm sorry to annoy you with my docking problems, but actually I can't
> understand if it's a software or hardware problem... Do you know why I
> obtain a so huge number of dihedral? Is there a way to limit this
sampling?
> I've yet tried to use the drive_id 3 and 4 according to the flex_drive.tbl
> achieving always a segmentation fault.
> 
> These are the last lines of the output using the standard flex.in docking
> definitions to dock a simple biphenyl molecule.
> 
>  -----------------------------------
> VERBOSE MOLECULE STATS
> 
>   Number of heavy atoms = 12
>   Number of rotatable bonds = 1
>   Formal Charge = -0.00
>   Molecular Weight = 154.21
>   Heavy Atoms = 12
> Orienting 7 anchor heavy atom centers
> -----------------------------------
> VERBOSE GROWTH STATS : ANCHOR #1
> 
> 118/992 anchor orients retained (max 1000) t=2.61s
> Lyr 1-1 Segs|
> Lyr:1 Seg:0 Bond:11 : Sampling 32649 dihedrals C2(C.ar)  C1(C.ar) 
C14(C.ar)
>  C13(C.ar)
>  
> Thank you again for your kind answers.
> Bye, 
> Marco
> 
> 
> ----
> Marco Cellanetti, 
> PhD Student.
> Bachelor Degree in Medicinal Chemistry and Technology of Drugs
> 
> University of Perugia
> Department of Medicinal Chemistry and Drug's Technology
> Via del Liceo, 1 - 06123 Perugia (Italy)
> Tel ++39 075 585 5169/5114


 
 
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