Senthil,
> yes, the structure is fine.. I don't see any problem in the coordinates.
That's good ;-) My wild guess is that given leap's internal method of
traversing the atoms, somehow some atoms are missed. Are the ones
that come close to the box in the protein, or the other molecules?
> Can you please comment on the usual way of doing it ?. Initially I
> tried to set up the system as Jan mentioned, preparing single pdb
> file but due to atom/residue numbering, it didn't work well.
I think atom numbering doesn't matter, but residue numbering could
be important. In which case the actual numbers may not differ so
much as making sure that adjacent residues have different numbers.
The case to be most concerned about is adjacent residues with the
same name and number. Maybe a TER between such residues (if chemically
appropriate) would be enough distinction.
> Probably due to too many ligand molecules (not at the same binding pocket) ?
I'd have to see the loadpdb output to guess.
> By looking at the structure, I could assume that the solvateOct
> somehow misplaced the solute as it is dragged towards one side.
Is clearance in the opposite direction correctly the 8A specified, or
twice that?
Bill
>
> Bill,
>
> 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?
>
> 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?
>
> 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.
>
> 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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Received on Wed Nov 09 2011 - 08:30:03 PST
