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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 16 2012 - 16:00:02 PDT
