ADL: I will be greatly thankful for the help

Daniel Jana dfjana at gmail.com
Sun Oct 21 02:25:30 PDT 2007


Hello Kala!

kala bharath wrote:
> 1.I couldnt able to run either autodock4 or autodock tools even after 
> modifying the .cshrc , when i run the "pmv" or 'ADT' it says "floating 
> point exception",     though when i type autogrid4, i could able to run 
> it - I feel that my hardware is insufficient, my configuration is
>   

What kind of shell do you use? Are you using csh? Since you are using 
Fedora I'd say your default shell is bash. If so you need to either 
change ".bashrc" or ".profile" (or some variant of the word). I would 
prefer to put the command in the ".profile" file (explaining it would be 
a bit more technical, but I would only go to ".bashrc" if ".profile" 
does not work).
That floating point exception occurred in Linux or Windows?

>     AMD Athalon 64 bit @ 1.8 Ghz speed
>     512 Mb RAM
>     K8V Mother Board with "VIA Unichrome S3 Graphics Adaptor"
>     " I am not having any "GRAPHIC CARD"  and the mother board has 64 mb 
> shared graphics"
>      Samsung 80 Gb SATA hard drive.
>     Fedora Core 5 x64 bit operating system , I also use x64 bit 
> operating system of Windows XP.
>   

While I can't tell the minimum hardware requirements because they are 
not presented in the website, and I have no access to the computers we 
have it installed in right now, I think that we are using both Autodock 
Tools and have use Autodock (through cygwin) in workstations with worse 
specifications. I can't recall correctly but I think one of our users is 
also using in a machine without a dedicated graphics card without 
problem. The dedicated graphics card should only influence in Autodock 
Tools, Autodock itself shouldn't depend on it. We don't have, however, 
run these programs in 64 bit computers so I can't tell you want to expect.


> 2. I failed to run ADT in my windows too. as soon as i start the 
> application my windows crashes with an appearance of "blue screen" with 
> a second my system restarts.
>   

Which version of ADT? Have you tried different versions?

> 3.What exactly needed to install to run autodock . Does the installation 
> of ADT is alone sufficient or should i have to install both the 
> autodock, autogrid and ADT. i am pretty confused with all these programs.
>   

ADT is the least needed. ADT is a visual aid to the building of the 
complex of interest and to the analysis of the results. In theory you 
could just read the output file directly.
For regular users (without computers for brain :D) you have to install 
all of them. Autogrid and Autodock will run the calculations, ADT will 
let you see the results (and make the inputs).

> 4.and also i couldnt able to install "Chimera" , from that i came to a 
> conclusion that there is something wrong with my graphics drivers.
>   

We don't have chimera at my lab. I may try tomorrow, if you want. 
However, the installation instructions seem quite simple. Since you have 
windows installed too, please try the windows version and see if you can 
use it. If so, then Linux should be also possible.
I don't think that programs do put you aside due to a bad graphics card 
(unless we are talking about video games). You may have though, very 
poor performance...
Which version of chimera did you try? Windows? Linux? Or Linux-x64?
They have installation instructions on the website. Please check if they 
help...

> 5.Please suggest me the essential hardware  and software upgrades , Also 
> the type and model of graphics card which i can install , and also with 
> the installation problems.
>   

Obviously a good graphics card would be helpful, since you are going to 
work with program that involve graphics in a way that a browser doesn't. 
However, I don't think you will need many hardware or software upgrades. 
If anything, only the 64 bit processor/operating system may be doing 
something, but I wouldn't think so.

Best of luck with this,
Daniel Jana


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