求问如何利用amber计算rmsd
求问如何利用amber计算rmsd，在官方教程上只看到了一些，但是看着很萌币，求助大神说下rmsd [<dataset name>] <mask> [<refmask>]
first | reference | ref <reffilename> | refindex <#>
]
Note: For backwards compatibility with ptraj the command ’rms’ will also work.
Calculate the RMSD between atoms in Frame defined by <mask> to atoms in Reference
defined by <refmask>. Both <mask> and <refmask> must specify the same number of atoms.
If no <refmask> is specified, <mask> is used for Reference. The Reference structure is defined
by one of the following keywords (of which only one should be specified):
1547.6 Action Commands
• first: Use the first trajectory frame processed as reference.
• reference: Use the first previously read in reference structure (refindex 0).
• ref: Use previously read in reference structure specified by <reffilename>.
• refindex: Use previously read in reference structure specified by <#> (based on order read
in).
If “nofit” is specified the Frame coordinates will not be best-fit to reference coords prior to
RMSD calculation. If “mass” keyword is specified the center of mass of atoms in <mask> will
be used, otherwise geometric center will be used. Example:
reference StructX.crd
reference Struct-begin.rst7
rmsd :1-20@C,CA,N reference :3-23@C,CA,N out rmsd1.dat
This will calculate the RMSD of the C, CA, and N atoms of residues 1 to 20 in each Frame to
the C, CA, and N atoms of residues 3 to 23 in StructX.crd (the first reference structure read in)
and write the results to rmsd1.dat. If instead of the reference keyword ’refindex 1’ was used,
Struct-begin.rst7 would be the reference structure instead. Note that if the number of atoms in
<mask> does not equal the number of atoms in <refmask> an error will be generated.
Per-residue RMSD calculation:
If the “perres” keyword is specified, after the initial RMSD calculation the no-fit RMSD of
each residue in each Frame specified by <resRange> (or all solute residues if range not
specified) will be calculated to each residue in Reference specified by <refRange> (or each
residue in <resRange> if reference range not specified), the results of which will be written to
the file specified by “perresout”. Note that in order to simplify output the residue range is
only set up based on the first trajectory/topology combination read in. By default all
atoms of each residue are used. An additional mask can be specified by using “perresmask”;
this mask is appended to the default mask of each residue (:X, where X is residue number). If
“perrescenter” is specified residues will be centered to a common point of reference before
no-fit RMSD is calculated (this will emphasize changes in the local structure of the residue).
So for example:
rmsd :10-260 refindex 0 perres perresout PRMS.dat range 190-211 perresmask &!(@H=)
will first perform an rms-fit calculation on residues 10-260, then calculate the per-residue no-fit
rmsd of residues 190 to 211 (excluding any hydrogen atoms).
If “perresinvert” is specified, data for each residue in <perresfile> will be written in rows
instead of columns, i.e.:
RES1 RmsdFrame1 RmsdFrame2 RmsdFrame3 ...
RES2 RmsdFrame1 RmsdFrame2 RmsdFrame3 ...
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