Hi,<br><br>I am trying to pull the first from the last amino acid of a
protein to completely unfold the protein in the X direction. I chose the
middle amino acid as the reference, and the groups get pulled in the
same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. <br><br>I define a different vector (pull_vec1 and pull_vec2)
with +x and -x values and that does not even pull the protein<br>I tried using only
pull_group1 and pull_group2, without a reference, and neither groups get
pulled. <br>I chose different references, I do have some success but I don't think it is the best way to do it.<br><br>How do I pull the N and C terminal apart, by simultaneously
pulling them in opposite directions?Why is my vector definition wrong? <br>
<br>This is my pull code:<br><br>pull = umbrella<br>pull_geometry = distance <br><br>pull_dim = Y N N<br>pull_start = yes <br>pull_ngroups = 2<br>pull_group0 = Chain-C<br>pull_group1 = Chain-B<br>
pull_group2 = Chain-A<br><br>%pull_vec1 = -31 0 0<br>%pull_vec2 = 31 0 0<br>pull_rate1 = 0.002 <br>pull_k1 = 1000 <br>pull_rate2 = 0.002 <br>pull_k2 = 1000 <br><br>
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Thanks!<br clear="all"><br>-- <br><div><br></div><i>"Every sentence I utter must be understood not as an affirmation but as a question." - Niels Bohr</i><br>