Dear Dan,
I tried running cpptraj using 'nobox' keyword with the trajout command' . It
works perfectly without segfault!!
Thank you very much!
Praapti
On Fri, Sep 16, 2011 at 10:40 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 Mon Sep 19 2011 - 23:00:04 PDT
