On 05/11/2011 06:24 AM, Frank Neuhaus wrote:
Hi,
I have a protein simulation in which all residues simulate correctly
with the exception of five in a loop. These five out of 360 are in a
loop (or bend) separate from my area of interest. Thus, I would like
to treat them as a rigid sequence. Using the position restraints in
the posre.itp file does not help me. I am looking for a script that I
can write into my mdp files that restricts all simulation in these
five residues. Can anyone help me with this little issue? Thank you.
What about their motion is not "correct"? If this is a disordered loop,
then probably your reference data for these residues is less reliable
than the MD simulation ensemble.
Mark
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