ADL: New Bug with another major one added.

ANURAG BAGARIA anurag.bagaria at gmail.com
Sun Jan 27 23:49:08 PST 2008


Dear Ruth,

I have been using MGLTools 1.4.6 and working on Linux OS (Ubuntu 7).
I invoke python scripts using the pythonsh command before calling the *.py
scripts. An additional information is that the invocation of python scripts
is working fine for most of the other *.py files in autodock4.

In addition to that when I try specifying the grid center manually into the
*.gpf files, there is yet another problem which is far more major than the
initial one (A greater bug indeed). When I finally run the autogrid4 program
using the gpf  file, the center point picked up by autogrid4 and specified
in the map files has constantly the same value for the X and Y
co-ordinates"CENTER 2.211 12.902 <Z>"; irrespective of the gridcenter value
that I specify in the gpf file. Moreover the value for Z co-ordinate changes
each time I run the autogrid4 command (Even when I keep the gridcenter value
constant). This is creating a major problem as this the point that is read
in as the Central Grid Point in the Docking Log file (dlg) and gives absurd
docking results. The X and Y co-ordinate values in "CENTER" of map files do
not change even when I re-dock a different receptor-ligand complex.

For further information I would like to inform that i have been using
autogrid4.0.0 and autodock4.0.1 for my purpose. I was wondering how this
problem has not been reported in the forum for so long.

Looking forward to positive response from the developers, users and members
of this team.

Warm regards.

On Dec 31, 2007 4:05 AM, <rhuey at scripps.edu> wrote:

> Hi,
>  I am able to say that it is working fine in my case because it is!
>
>  I will be happy to try and debug what is not working for you if you
> would please tell me:
>  1. which version of MGLTools you are using,
>  2. what platform (os) you are working on,
>  3. how you invoked the python script
>
>  Thank you for your interest in our tools and for your feedback!
>
>    Ruth
>
> > Yesh, the bug is still there. I don't know how ruth was able to say it
> is
> > working fine in his case.
> >
> > On Dec 28, 2007 6:37 AM, ANURAG BAGARIA <anurag.bagaria at gmail.com>
> wrote:
> >
> >> Hi Members and Visitors of this group,
> >>
> >> I am using Autodock4 on Ubuntu platform but am unable to specify the
> >> gridcenter co-ordinates through the "-p" flag. I found a description
> >> regarding the same while going through one of the "How to(s)" at :
> >>
> >>
> >>
> http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-grid-parameter-files-for-autogrid4
> >>
> >>
> >>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >> Known problems To specify coordinates for the parameter *gridcenter*,
> it
> >> is
> >> necessary to enclose them in quotation marks like this:
> >>
> >> *prepare_gpf4.py -l ind.pdbqt -r hsg1.pdbqt -p gridcenter='1.0 2.0
> >> 3.0' -o test.gpf*
> >>
> >>
> >>
> >>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >>
> >> BUT, still the problem persists as only the x co-ordinate gets
> specified
> >> this way. I have tried all possible permutation and combinations by hit
> >> and
> >> trial but NO success so far. Can someone help me out of this bug.
> >>
> >> Thanking you all in advance and with warm regards.
> >> --
> >> The road to success is always under construction ...!!!
> >>
> >>
> >> ANURAG KUMAR BAGARIA
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
>
>


-- 
The road to success is always under construction ...!!!


ANURAG KUMAR BAGARIA

Member of Research Team
Lead Invent Technologies Pvt. Ltd.
Technology Business Incubation Unit
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi - 110016


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