very helpful, thanks J.
(grabbing in moving was just so much fun though..... Maybe when I have a
clue I'll figure something out)
On Sat, Jun 16, 2012 at 6:34 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sat, Jun 16, 2012 at 4:45 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > Hey All,
> >
> > I'm having a blast playing with amber thus far!
> >
> > However, I could use some insight from those who are more experienced.
> >
> > What I want to do:
> > create a peptide polymer (minimize it). Then duplicate it and place it's
> > clone(s) near (not on top) the original. Then create the necessary
> .prmtop
> > and inpcrd files so I can play.
> >
>
> Here's something that may work. Create the peptide polymer (using the
> "sequence" command, for instance), and create the .prmtop and .inpcrd. Do
> what you need to to it. Take the final restart, save it as a PDB using
> ambpdb.
>
> Here's where you can do a couple different things. Load it into tleap,
> make a copy of it, then translate that unit by some given amount. So
> assuming your PDB you got from ambpdb in the last step is named X.pdb,
> something like this (look at the manual and play around):
>
> mol = loadpdb X.pdb
> mol2 = copy mol
> translate mol2 {5 5 5} # this moves the coordinates +5x +5y +5z.
> bigmol = combine {mol mol2}
>
> saveamberparm bigmol prmtop inpcrd
>
> Here is where things when awry:
> > used avagadro to duplicate said pdb and rearrange things. saved it as a
> > pdb file (it runs on open babel). tried to read the pdb file in via
> xleap
> > - no good.
> >
>
> Avoid avogadro for this type of thing when possible -- it messes up atom
> names (it's better for small molecules you run through antechamber, not so
> much for proteins and nucleic acids).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sat Jun 16 2012 - 16:00:03 PDT
