Dear RG experts,
I'm playing with Meta dynamics for the first time and I'm struggling to come up with a way of rotating my ligand in the catalytic site of an enzyme. The ligand is a long narrow peptide, an alpha helix embedded within the catalytic site. I want to investigate the possibility of non-specific binding using the metadynamics capabilities of PLUMED patched onto Gromacs. I am currently trying the idea of defining four points, two on the ligand and two on the enzyme, then using them to define a torsion angle.
I've trawled the literature and I only seem to find 'in house' or mathematics to define specific actions or rotation/spin of one protein against the other. Unfortunately, none of these have been implemented in PLUMED as far as I can see.
I would really appreciate and thoughts on this problem.
Thanks
Anthony
Hi Anthony,
If I understood your problem correctly, you are trying to invert the position of peptide in order to perform MD of this inverted position inside the catalytic site. And you are facing problem in inverting the peptide.
But my question is why specifically you wanted to perform the rotation from plumed. You can simply rotate the coordinates by mathematical formulas for rotating a vector.
Let me know if there is more to it.
Cheers!!
Hi Anupam,
I want to rotate the ligand in the catalytic site using PLUMED so I can perform metadynamics and thus plot of free energy surface. Alternatively, if Gromacs can perform a rotation for me (as per the first reply) I can use that trajectory to then perform umbrella sampling.
Hi, if you want to study the relative stability of the ligand in two different poses, you can exploit different approaches using PLUMED since you have the two end-point configurations:
1. (S) and (Z) paths, http://plumed.github.io/doc-v2.1/user-doc/html/_f_u_n_c_p_a_t_h_m_s_d.html and http://plumed.github.io/doc-v2.1/user-doc/html/_p_a_t_h_m_s_d.html
2. RMSD http://plumed.github.io/doc-v2.1/user-doc/html/_r_m_s_d.html
you can even perform a commitor analysis: http://plumed.github.io/doc-v2.1/user-doc/html/_c_o_m_m_i_t_t_o_r.html
hope it helps
and
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