Dear Amber Users
I want to calculate interaction energy between two urea molecules in
homogeneous urea solution (only urea molecules are there). For that I used
antechamber modules to generate urea "prep" and "frc" file. The generated
file contain GAFF force field parameter. After production MD run, I process
the trajectory to calculate pairwise interaction energy. I used the
pairwise command but I am getting + 36.34 kcal/mol while the reported
theoretical value for dimer is -10.33 kcal/mol (MP2/aug-cc-pVDZ).
I am using "CPPTRAJ: Trajectory Analysis. V13.0".
Is there are bugs in this command??
Please also suggest me any other way to calculate residue wise pair
interaction energy.
Thank you in advance for your help
Rahman
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*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785 <%2B91-%207845991785>*
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Received on Fri Sep 05 2014 - 08:30:02 PDT
