AMBER Archive (2009)

Subject: Re: [AMBER] Single Adenine

From: ros (ros_at_servidor.unam.mx)
Date: Wed Aug 26 2009 - 12:50:54 CDT

Hello!
Thanks for the help! I have a single adenine working with parm and top files
made from tleap.

Quick question, what is the best way to add two molecules so they can
interact?
1- Make a pdb with both molecules and then do all the fiddling of external
parameters in tleap
2- Join somehow directly on tleap once each molecule has its external
parameters loaded

Any guide will be great!
Thanks again!

ros.

2009/8/26 case <case_at_biomaps.rutgers.edu>

> On Wed, Aug 26, 2009, case wrote:
> > On Wed, Aug 26, 2009, ros wrote:
> >
> > > I am trying to study the interaction of a Cu(II) compund with adenine.
> I
> > > have working prmtop and inpcrd for the metal-compound but cant get a
> single
> > > adenine molecule to work. I tried using the residues from the force
> fields
> > > (DA, DA3, DA5, etc) but these are the full nucleotide. So I tried
> drawing
> > > one by hand and relaxing the structure using g03, exporting to PDB and
> using
> > > antechamber to generate the frcmod file. When I fire up xleap and load
> the
> > > adenine.pdb, it gets recognized as DA3 and displays broken bonds and
> missing
> > > atoms.
> >
> > First, the pdb file would only be "recognized as DA3" if its name is DA3.
> So,
> > you might just need to change the residue name in the pdb file. Second,
> DAN
> > (the deoxy adenine nucleoside) is probably closest to what you want.
>
> Just another thought: it's not clear from the post exactly what you mean
> by
> "fire up xleap and load the adenine.pdb": pdb files don't have connectivity
> information, so this might be what is expected. If you have been through
> antechamber, you need to load the resulting mol2 or prep file that was
> created
> in antechamber.
>
> ...dac
>
>
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>
> 

-- 
ros
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