On Mon, 2014-06-02 at 15:47 +0900, yjlee wrote:
> Thank you for your response and cares, Soumendranath.
>
>
> As I understand, the CPPTRAJ script that you wrote convert one of the
> frame written in the mdcrd file to pdb file, after taking the water
> molecules and Na+ ions away, right?
>
> I did similar thing, using restart file and PTRAJ program. It looks
> like,
> however, I still have the problem.
>
>
> For my case, there are only water molecules so I didn't strip out
> the water molecules. Also I have individual restart files for each
> frames of NVT simulation.
>
> Here's the PTRAJ script I used
>
> trajin /home/yjlee/amber/purewater/rsts/NVTmd.rst_####
> trajout ./####.pdb pdb
> go
>
> I did same thing, changing the #### to restart file name (which
> corresponds
> to the frame number) and loaded the pdb files with VMD. Still the
> problem occurs.
>
>
>
> ONE THING THAT CONCERNS ME IS the "autoimage" command in your script.
> Since you
> said it seems to be imaging problem, this command might be the
> solution.
>
> So I tried with your script, using CPPTRAJ, like this
>
> trajin /home/yjlee/amber/purewater/rsts/NVTmd.rst_####
> autoimage
> trajout ./####.pdb pdb
>
> but when I run the CPPTRAJ, I found that CPPTRAJ doesn't know
> "autoimage" command.
>
> [autoimage]
> Warning: Unknown Command autoimage.
>
> I couldn't find "autoimage" on ambertools manual file also.
>
>
>
> Could you, anybody, give me some suggestion?
You must be using a very old version of cpptraj. Upgrade to the latest
AmberTools release.
Also, if you don't want waters (or ions) in your PDB file, you need to
strip those out using the "strip" command. All of this described in the
latest Amber 14 manual (that comes with the AmberTools 14 download).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 02 2014 - 04:30:04 PDT
