Dear Dan,
thanks for your email
I was confused with what i have read in Ambertools12 manual, thinking that by omitting the "nobox"
box coordinates will be written to the pdb file
on page 173 of the Ambertools12.pdb manual i copied the following :
The file will be appended to if append is specified (only supported Amber trajectory and
Amber netcdf trajectory). Box coordinates will not be written if nobox specified (only matters
when input topology has box coordinates). Associate with parameter file specified by parm
<parmfile> or parmindex <#> (first parm read in if not specified). The output trajectory title
can be set using the title keyword.
Multiple output trajectories of any format can be specified. Currently frames will be written
many thanks
Fatima
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Monday, April 20, 2015 4:04 PM
To: AMBER Mailing List
Subject: Re: [AMBER] cpptraj writting box coordinates issue
Hi,
Writing box coordinates to PDB files is not supported by current
cpptraj versions. It will be supported (via a CRYST1 record) in
cpptraj version 15, part of the upcoming AmberTools 15 release.
-Dan
On Mon, Apr 20, 2015 at 9:00 AM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
> Dear all
> I am using the following version of cpptraj to output a pdb files from an mdcrd trajectory file containing box coordinates
> CPPTRAJ: Trajectory Analysis. V13.22
>
> so I run the following
>
> cpptraj < cpptrajin.in
>
> cat cpptrajin.in
>
> parm prmtop
> trajin mdrun.mdcrd
> trajout 8cbcm4_5odespBn_md2-boxg.pdb pdb append
>
>
> I do not get any box coordinates written to the pdb file
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Apr 20 2015 - 08:30:03 PDT
