Dear Amber Users,
I am doing a work using AMBER12 with a protein in water at 400K
temperature. I want to see the thermal denaturation of the protein having
130 residue.I have already calculated the RMSD and radius of
gyration (Rg) of that protein. The RMSD value is matching well with
the reported value. But the radius of gyration is decreasing
inspite of breaking of the secondary structure of that
protein. And the breaking of secondary structure of the protein is
very clear from RMSD as well as secondary structure calculation
also. But the anomaly is happening with the Rg value which should
not happen at all. When a protein unfolds totally then its Rg
value should go beyond 17-18A which is reported in many
literatures. If you kindly check my inputs whether I am doing
right or wrong as I am doing these by CPPTRAJ program then it will be
great pleasure to me.
I have attached the input file as well as the graphs in attachment.
I will be highly obliged if you kindly help me to figure out the problem.
Thanking you.
Krishna
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Received on Tue Sep 26 2017 - 09:30:03 PDT
