[gmx-users] Script for coverting ITP and gro file to Autodock pdbqs

[raja]

Hi Mahnam,
Thanks for your mail. Sorry, I do not get you whether you are talking on
charge based on individual residue or on whole protein. As for as I
know, autodock is not allowing non integer charge on residue basis and
which implies that whole protein can also, should not have non integer
as net formal charge and zero is not mandatory.

Please reply me.

B.Nataraj



On Wed, 29 Nov 2006 19:16:52 +0330, "Mahnam" <mahnam at ibb.ut.ac.ir> said:
> In God We Trust
> Hello Dear raja
> I think that the charges in itp of Gromacs don't match with charges in
> Autodock.Becase the total charge in Autodock is zero ,but the total
> charges in itp of Gromacs are not zero ,then you can't use gromacs charge
> for Autodock. 
>  
> Sincerely yours
> Karim Mahnam
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University 
> P.O.box 13145-1384
> Tehran 
> Iran 
> http://www.ibb.ut.ac.ir/
> 
> 
> 
> -----Original Message-----
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Tue, 28 Nov 2006 12:47:14 +1100
> Subject: Re: [gmx-users] Script for coverting ITP and gro file to
> Autodock
> pdbqs
> 
> > raja wrote:
> > > Hi gmxions,
> > > I want to use charge information contained in itp file produced in
> > > gromacs for docking purpose (Autodock). Kindly share a script if
> > anyone
> > > written to convert information content from gromacs protein's itp
> > (for
> > > charge) and gro (coordinate) information to autodock pdbqs or pdbq
> > > formated one.
> > 
> > This sounds like a good exercise for learning how to use Perl. Get the 
> > file format descriptions and read a few chapters of a Perl reference.
> > 
> > Mark
> > _______________________________________________
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> 
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-- 
  raja
  raja_28 at fastmail.us

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