Bill,
>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?
yes they are protein atoms
>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.
I modified the residue numbers and put TER line too.. still giving errors.
>I'd have to see the loadpdb output to guess.
please look at my previous email
>Is clearance in the opposite direction correctly the 8A specified, or
twice that?
yes I measured distance ~ 16-18 A
thanks,
Senthil
>
> 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 - 11:30:07 PST
