Dear Amber User's
I am trying to calculate distance based energy between protein and first
hydration layer. For that I am using energy modules of cpptraj as given
below
parm traj.parm7
trajin traj.nc
reference traj.nc
energy Protein_Water :1-20|(:1-20<:3.5)&:WAT out sys1_traj.dat
nb14 nonbond elec vdw etype simple
energy Protein_Protein :1-20 out
sys1_traj.dat nb14 nonbond elec vdw etype simple
energy Water_Water (:1-20<:3.5)&:WAT out sys1_traj.dat
nb14 nonbond elec vdw etype simple
Here I am giving same trajectory as reference for selecting distance based
atoms mask. But after running this cpptraj taking first frame of reference
trajectory.
I have many systems to calculate energy for whole protein and with each
amino acid that why I am not using strip command here.
my question are
1) how to assign reference so that it will update with each frame of
trajectory?
2) For energy calculation the assign mask for water-water is correct.
Thank you in advance
Regards
Rahman
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
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Received on Thu Sep 13 2018 - 07:02:36 PDT
