Dear JIomm,
> I have joined the residues by defining head and tail atoms and sequence
> command in tleap. the system is macromolecule like. so is there any
> limit of number of residues that can be added.
If you use the "sequence" command of LEaP to create a very long
peptide sequence, the conformation will be extended. If you solvate
the corresponding system the box size will be quite huge...
You might try to follow a different approach. Use a builder different
to LEaP to generate a PDB file that you will load in LEaP in a second
step. For instance insightII under SGI can do this job. I am sure you
can find other tools to do that...
Or you might try to build your peptide using a different approach in
LEaP. I did a quick test:
a = sequence { GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY }
b = sequence { a a a a a a a a a a }
c = sequence { b b b b b b b b b b }
desc c
=> I get 1000 GLY residues without any problem.
did I miss something ?
regards, Francois
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Received on Thu Feb 11 2010 - 03:00:02 PST
