Hi,
Sometime ago, i asked the same question as i want to do the same. I was
suggested to use pakmol to prepare the input file for amber. It will give a
.pdb file that can be used in AMBER. there is a tutorial on the AMBER
website on ionic liquids for basic understanding.
I still have not tried it but intend to.
regards
ayesha
On Thu, Apr 24, 2014 at 8:07 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Apr 24, 2014, Fabian Glaser wrote:
> >
> > I am interested to calculate the free energy of interaction on many
> > frames of MD for two drug like molecules, I plan the following:
> >
> > 1) Prepare the molecules with antechamber
> > 2) Run MD in vacuum or water
> > 3) Calculate MM-PBSA as you did for a protein-ligand on
> > http://ambermd.org/tutorials/advanced/tutorial3/
>
> >
> > Is that a good idea for two copies of drug molecules (e.g. RITONAVIR)?
>
> In principle, it doesn't matter what the "ligand" and "receptor" are: they
> could both be drug molecules. But is seems likely that the two drug
> molecules
> may move apart from each other during the MD simulation, which will lead
> to a very small free energy of interaction. But perhaps the molecule is
> known to dimerize(?)
>
> ....dac
>
>
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Received on Thu Apr 24 2014 - 05:30:05 PDT
