Hi,
I am interested in comparing the normal modes of a protein with and
without a ligand. I have already computed the lowest 100 normal modes
for the protein (eigenvec_a.trr) and the protein:ligand complex and
have reduced the protein:ligand eigenvec_b.trr to the protein by
issuing;
> trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr
> select 0 [System]
Where:
+ nm_a.tpr is the tpr file of the protein alone
+ eigenvec_b.trr is the trajectory of the protein:ligand
+ eigenvec_c.trr is the new trajectory of the complex minus the
ligand coordinates
What I want to do now is compare the eigenvec_a.trr and
eigenvec_c.trr files to see the mode overlap between the free and
bound protein.
What I can not understand how to remove the effects of rotation and
translation of the protein with respect to the ligand that will be
present in the eigenvec_c.trr. Is it possible to do this type of
analysis in GROMACS and how can I go about it?
Regards,
Bryn
==========================================================
R. Bryn Fenwick Department of Biochemistry,
[EMAIL PROTECTED] University of Cambridge,
[EMAIL PROTECTED] 80 Tennis Court Road,
Tel: +44 1223 766018 Old Addenbrookes Site,
Fax: +44 1223 766002 Cambridge, CB2 1GA, UK.
==========================================================
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