Dear Users,
For xplor file generation, this is my input file
parm /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/3kfa_layer_ACN_H2O_5-95vv.prmtop
trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4E_production.1.crd 1 1250 1
trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4F_production.1.crd 1 1250 1
autoimage
#Align trajectory to reference structure by minimizing RMSD
reference /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/setup_solvbox/3kfa_layer_ACN_H2O_5-95vv.pdb
strip :Cl-,Na+
rms reference mass out 3kfa_ACN_10-15ns_md_CA_rmsd.txt :1-286.CA
#Write out grid count of probe occupancy
grid out 3kfa_ACN_10-15ns_C3N.C3.xplor 200 0.5 200 0.5 200 0.5 :C3N.C3 origin max 0.9
grid out 3kfa_ACN_10-15ns_C3N.C2.xplor 200 0.5 200 0.5 200 0.5 :C3N.C2 origin max 0.9
grid out 3kfa_ACN_10-15ns_C3N.N.xplor 200 0.5 200 0.5 200 0.5 :C3N.N1 origin max 0.9
#Correct for systematic error induced by ptraj grid function
translate x -0.25 y -0.25 z -0.25
#Calculate Average Structure
average 3kfa_avg_ACN_10-15ns.pdb :1-286 pdb append
go
This works for acetonitrile as we know its symmetric and the central atom is C2 carbon.
However, for pyrimidine if I have to do Center of mass binning cpptraj does not do that or am I missing something?
Please help.
Thanks
Debarati
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Received on Wed Feb 27 2019 - 13:00:02 PST
