In your first step you are creating a trajectory with stripped
coordinates (model_wat_md.mdcrd) and in your second step you are
trying to read the stripped coordinates using a topology file for the
non-stripped system (model_wat.prmtop). You need to create a topology
file that matches the stripped trajectory and use that for your second
ptraj run.
Also, it appears you are using ptraj from amber 9. I highly recommend
you upgrade to ptraj from AmberTools 1.4 as it performs better and
contains numerous bug fixes: http://ambermd.org/#AmberTools.
-Dan
On Wed, Sep 1, 2010 at 5:05 AM, Ehsan Habibi <EHabibi.ibb.ut.ac.ir> wrote:
> Dear Amber specialist,
> I don't have any experience in checking hydrogen bonds but I
> intend to check for changes in hydrogen bonds of a dimer protein (two
> monomer with 55 aa) in protein-DNA complex with 170 residues (1-110 aa
> & a 30-mer DNA (111-170)).
> I created a .ptraj file (model.ptraj)
> containing
>
>
> trajin model_wat_md2.mdcrd 1
> 1000 5
> trajout model_wat_md.mdcrd
> center
> :1-110
> strip : WAT
> go
>
> and I issued the following command:
>
> ./ptraj
> model_wat.prmtop < model.ptraj
>
> then, to abstract hydrogen bonds I created
> an .in file. Attached I am
> sending the file. But when I issue the following command:
>
> ./ptraj model_wat.prmtop
> <ptraj.1.in> ptraj.1.out
> the
> following message appear on screen and it last for a long time without any
> action
> checking coordinates:
> /root/amber9/exe/model_md.mdcrd
> Does it wrong?
> what's wrong with me?
> would you please help me?
> Regards,
> Ehsan
>
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Received on Wed Sep 01 2010 - 05:30:04 PDT
