Carlos, Daniel many thanks.
Daniel, I need to compile cpptraj. I shall do so shortly. I'm following your instructions
http://dev-archive.ambermd.org/201107/0005.html
unless otherwise advised by you.
As concerns my last question (re ptraj scanning mdcrd files not specified in the trajin line), please consider it redundant. I must have been doing something wrong.
Best regards
George
On Jul 18, 2011, at 6:19 PM, Daniel Roe wrote:
> Hi,
>
> On Mon, Jul 18, 2011 at 12:00 PM, George Tzotzos <gtzotzos.me.com> wrote:
>> Is there a way to produce only one new.pdb file?
>
> If your intent is to create a single PDB file containing all of your
> frames you can either write a script that will concatenate all of your
> PDB files into a single file separated with MODEL X and ENDMDL
> keywords, or just use cpptraj (this is the default way cpptraj writes
> out PDB files).
>
> If your intent is to only write 1 frame, you need to specify that in
> your trajin command - numeric arguments are not processed for trajout
> commands:
>
> trajin prod_2ns.mdcrd 1 1
> trajout test.pdb pdb
>
> If you want to write out your entire trajectory as netcdf AND write
> only 1 frame of PDB, you need to use cpptraj and the 'onlyframes'
> keyword:
>
> trajin prod_2ns.mdcrd
> trajout test.pdb pdb onlyframes 1
> trajout prod_closest_WAT_2.mdcrd netcdf
>
> This will create a PDB file containing only the first frame from
> prod_2ns.mdcrd, as well as the specified output netcdf trajectory
> containing all frames. Note that cpptraj does not use the "solvent"
> command (right now solvent is assumed to be named :WAT so your script
> should still run fine in cpptraj).
>
>> Furthermore, if the working directory contains other trajectories (e.g. prod_4ns, prod_6ns, etc.), the script scans them all - although they are not specified in the first line of the script. Any suggestions why so?
>
> This should not happen. Are you executing this as part of a larger
> shell script? The trajin command of ptraj should only process the file
> it is given. If you can, please post your entire ptraj output as an
> attachment.
>
> Let me know if you have any more questions.
>
> -Dan
>
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Received on Mon Jul 18 2011 - 10:00:04 PDT
