Hi,
>From your output I can see a couple of problems:
> CPPTRAJ: Trajectory Analysis. V1.0.5
Version 1.0.5 is the unpatched version of cpptraj. The latest version
after applying all AmberTools 1.5 bugfixes
(
http://ambermd.org/bugfixesat.html) should be V1.1.1.
> INPUT: Reading Input from file ptraj_res_rmsd.in
> [trajin wt1mg_dry.mdcrd]
> Warning: Box coords detected in trajectory but not defined in topology!
> Setting box type to rectangular.
Your input trajectory (wt1mg_dry.mdcrd) contains box coordinates, but
your topology (wt1mg_dry.prmtop) does not. To avoid printing box
information in your output trajectory when stripping solvent use the
'nobox' keyword with the trajout command.
> [reference wt1mg-ref.pdb]
> Warning: wt1mg-ref.pdb: Atom 10 name [HG ] does not match parm name [HSG ]
> ERROR: PDBfile::SetupRead(): No frames read. atom=2380 expected 2381.
> ERROR: Setting up wt1mg-ref.pdb for read.
It appears that your reference PDB does not contain the same number of
atoms as your input topology (wt1mg_dry.prmtop). You can just use the
PDB file as its own topology file, e.g.
parm wt1mg-ref.pdb
reference wt1mg-ref.pdb parm wt1mg-ref.pdb
This will direct cpptraj to read wt1mg-ref.pdb as a reference using
parameters obtained from wt1mg-ref.pdb rather than the first topology
file. Take care however that any atoms you specify in your mask
correspond to atoms in your reference. If necessary, you can specify a
separate reference mask for the rms command (and the perres
functionality) - see the AmberTools manual for details.
So to summarize the above comments, first upgrade your AmberTools
installation, consider re-stripping your trajectory with the 'nobox'
keyword, and try using the following cpptraj input (adding a reference
mask and 'refrange' argument to the rms action if necessary):
trajin wt1mg_dry.mdcrd
parm wt1mg-ref.pdb
reference wt1mg-ref.pdb parm wt1mg-ref.pdb
rmsd :1-154 reference perres range 1-154 perresout all-back.tmp
perresmask .CA,C,O,N
-Dan
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Received on Thu Sep 15 2011 - 22:30:02 PDT
