ADL: regarding active site (for Davide)

Gnanasekar Gopal ggmacro at yahoo.com
Fri Jun 19 00:29:38 PDT 2009


Dear Davide,

It is not a problem. I think no need to remove your autodock-vina from your computer. You can download the autodock4 software and install in your computer. Before autodock4 downloading, you should install Cygwin software.

Cheers,
G.G




________________________________
From: Davide Mercadante <dmer018 at aucklanduni.ac.nz>
To: autodock at scripps.edu
Sent: Wednesday, June 17, 2009 2:22:44 PM
Subject: Re: ADL: regarding active site

Dear Dr. Oleg Trott,

thanks infintely for your help. I will try using autodock-vina to see if I
am able to solve the problem. I have autodock 4 now installed on my machine.
Should I remove it before installing Autodock-Vina or can I just go through
the installation of autodock-vina without removing autodock4?

Thanks again,

Cheers,
Davide

2009/6/16 Oleg Trott <trott at scripps.edu>

> David,
>
> What problem are you referring to? If it's ligands going far outside
> the search space then, like I just wrote, I don't think it will happen
> in Vina.
>
> Oleg
>
> On Sun, Jun 14, 2009 at 1:30 PM, Davide
> Mercadante<dmer018 at aucklanduni.ac.nz> wrote:
> > Dear Oleg,
> >
> > sorry for the late reply. I am using Autodock 4 and not Autodock Vina.
> So,
> > do you advice me to use Vina?
> >  Do you think I will be able to solve the problem?
> >
> > Cheers,
> > Davide
> >
> > 2009/6/14 Oleg Trott <trott at scripps.edu>
> >
> >> On Fri, Jun 12, 2009 at 3:53 PM, Davide
> >> Mercadante<dmer018 at aucklanduni.ac.nz> wrote:
> >>
> >> > 2) After the calculations the docked ligands are not in the box that I
> >> built
> >> > to perform the calculation
> >>
> >> Are you using AutoDock 4 or AutoDock Vina? In Vina, there is a stiff
> >> scoring function penalty for going outside the box, so the ligand is
> >> very unlikely to stray too far.
> >>
> >> Oleg
> >> --
> >> Oleg Trott, Ph.D. (Columbia University)
> >>
> >> http://olegtrott.com
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> http://olegtrott.com
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
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