Dear Amber straff
for rmsd caculation via cpptraj I try to use this below script.
trajin ../../eq/md/5xxx_md45.nc
trajin ../../eq/md/5xxx_md46.nc
trajin ../../eq/md/5xxx_md47.nc
trajin ../../eq/md/5xxx_md48.nc
trajin ../../eq/md/5xxx_md49.nc
center :1-325,326 mass origin
image origin center
reference ../../5xxx.rst7
rms reference :1-325,326 out protein_ligand_100ns.rms
rms reference :1-325 out protein_100ns.rms
rms reference :326 out ligand_100ns.rms
rms reference :1-325.CA,C,O,N out protein_backbone_100ns.rms
and also this script
trajin ../../eq/md/5xxx_md45.nc
trajin ../../eq/md/5xxx_md46.nc
trajin ../../eq/md/5xxx_md47.nc
trajin ../../eq/md/5xxx_md48.nc
trajin ../../eq/md/5xxx_md49.nc
autoimage
reference ../../5xxx.rst7
rms reference :1-325,326 out protein_ligand_100ns.rms
rms reference :1-325 out protein_100ns.rms
rms reference :326 out ligand_100ns.rms
rms reference :1-325.CA,C,O,N out protein_backbone_100ns.rms
When I finished the ligand and backbone protein's result showed
#Frame RMSD_00004
1 0.0000
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000
8 0.0000
9 0.0000
10 0.0000
11 0.0000
12 0.0000
13 0.0000
14 0.0000
15 0.0000
but for protein's result it show the rmsd value.
When I saw the .log I found
----- 5lrnD_md49.nc (1-200, 1) -----
Too many iterations in routine!
Convergence failed.
Too many iterations in routine!
Convergence failed.
Too many iterations in routine!
Convergence failed.
Too many iterations in routine!
Convergence failed.
Too many iterations in routine!
So I didnt sure that can I trust the protein RMSD result?
and What's happen? for another result
Or I miss something for RMSD's script.
Have you found the error like this? Could you suggest me How can I solve this problem?
Best wishes,
Kungking
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Received on Sat Apr 29 2017 - 02:30:02 PDT
