Hi Jan-Philip,
>
> I am still quite new to Amber things and have used leap in the same way
> as Senthil did in order to set up a protein-ligand complex. Hence, I
> used something like:
>
> p = loadpdb protein.pdb
> l = loadpdb ligand.pdb
> c = combine {p l}
> [addions, solvateoct, saveamberparams]
>
> The system was built and simulated properly this way. I am wondering why
> this should be an unusual way. Do most people set up PDB files with the
> entire complex before starting leap?
That was the original way we planned. I don't know what people are
doing in general.
> If combine works well for two objects, shouldn't it perfectly upscale
> with more items? Also, why should it matter to the solvation code how
> the set of coordinates it receives as input has been created?
To calculate the box, one has to iterate over all the atoms. If some
atoms are closer than cut to the edge of the box, then it sounds as
if they were missed. Since combine wasn't tested during development,
I speculate this could be the source of the problem. But not having
looked at the code for 10 years, I am just speculating.
>
> It would be nice to see if the solvation behavior changes when Senthil
> prepares his complex in one big PDB file and skips the combine step. I
> don't hope so.
We will see..
Bill
>
> Jan-Philip
>
>
> On 11/09/2011 12:05 AM, Bill Ross wrote:
> > Hi Senthil,
> >
> >> complex = combine {protein HQN MYR1 MYR2 MYR3 MYR4 MYR5 MYR6}
> >
> > This is unusual - if you just 'savepdb complex' at this point,
> > is the structure reasonable? Maybe the default coordinates of
> > all these units would fall in the right place without loadpdb
> > assigning them, but if so I would be surprised. But even in
> > that case, you are taking a route for building the system that
> > few have used before, I believe, and this could explain why it
> > hasn't been seen before. Certainly it is one that I never thought
> > to test.
> >
> > Bill
> >
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>
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Received on Wed Nov 09 2011 - 07:00:04 PST
