1.
ptraj
command to calculate rms with refernce PDB:
reference bdna3_wat_rand.pdb
center :1-24 mass origin
image origin center familiar
strip :WAT
strip :Na+
rms reference out 10ns_bdna_for_ref_B.rms :1-24 time 0.5
go
2.
ptraj
command to calculate all atom rms
trajin
bdna_md2.9220_9420.mdcrd
trajin bdna_md2.9420_9620.mdcrd
trajin bdna_md2.9620_9820.mdcrd
trajin bdna_md2.9820_10020.mdcrd
trajout 10ns_bdna_all_atom_rmsd.mdcrd
center :1-24 mass origin
image origin center familiar
rms first out 10ns_bdna_all_atom_rmsd.rms :1-24 time 0.5
go
3.
ptraj
command to calculate all atom rms with out terminal base
pairs
trajin
bdna_md2.9220_9420.mdcrd
trajin bdna_md2.9420_9620.mdcrd
trajin bdna_md2.9620_9820.mdcrd
trajin bdna_md2.9820_10020.mdcrd
trajout 10ns_bdna_all_atom_rmsd.mdcrd
center :2-11,14-23 mass origin
image origin center familiar
rms first out 10ns_bdna_all_atom_rmsd.rms :2-11,14-23 time 0.5
go
4. ptraj
command to calculate all atom rms with out terminal base pairs(for
pdbid
-10mer)
trajin
pdbid_md2.0020_0220.mdcrd
trajin pdbid_md2.0220_0420.mdcrd
trajin pdbid_md2.0420_0620.mdcrd
trajin pdbid_md2.0620_0820.mdcrd
trajin pdbid_md2.0820_1020.mdcrd
trajin pdbid_md2.1020_1220.mdcrd
trajin pdbid_md2.1220_1420.mdcrd
trajin pdbid_md2.1420_1620.mdcrd
trajin pdbid_md2.1620_1820.mdcrd
trajin pdbid_md2.1820_2020.mdcrd
trajout 10ns_pdbid_all_atom_tercut_rmsd.mdcrd
center :1-20 mass origin
image origin center familiar
rms first out 10ns_pdbid_all_atom_tercut_rmsd.rms :2-9,12-19 time 0.5
go
5.
Generate PDB's from the trajectory
Step 1: follow
Intsruction 2
Step 2: strip water and ions and generate PDB's
trajin 10ns_pdbid_nowat_noion.mdcrd
strip :21-9999999
trajout pdbid_10ns_pdb pdb
go
AMBER 9:
if NTT=2 or 3
using ig=<random
5 digit prime number>
Ref:
http://structbio.vanderbilt.edu/archives/amber-archive/2009/1287.php
Explanation on MD simulation.
http://structbio.vanderbilt.edu/archives/amber-archive/2008/4793.php