Thanks Dan,
For such a quick reply. I removed the bracket and also modified the script
and now the property of output file is almost double in size..
* min2.rst ---> 2392805
new.rst.1 --->4785551*
This time I am able to generate the the pdb and got the desired result. But
I am surprised about the so much increment in file size.
Thanks,
Hirdesh
On Tue, Feb 8, 2011 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> I think what has happened here is you want to write new.rst as an
> Amber restart file but are actually writing it as an Amber trajectory
> (you can double check your ptraj output to see if this is the case).
> If no format keywords are specified with the 'trajout' command it
> defaults to Amber trajectory. Try:
>
> trajout new.rst restart
>
> and see if that works. Also, I don't think you need the brackets in
> the 'translate' command.
>
> -Dan
>
> On Tue, Feb 8, 2011 at 12:02 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
> > Hi All,
> > I was trying to change the coordinate of one of the atom in my trajectory
> > file using ptraj. Below mentioned is the script for same:
> >
> > *trajin min2.rst
> > translate .5258 [x -0.294] [y 0] [z 0]
> > trajout new.rst
> > go*
> >
> > I want atom number 5258 to change in 3d for its X coordinate. When I
> check
> > for the property of input and output file I found
> > * min2.rst ---> 2392805 Byte
> > new.rst ---> 1593018 Byte*
> >
> > I have done something wrong as just the change in one coordinate cant
> change
> > the file size to this much extent. To further check the result, I
> prepared
> > the pdb file using output trajectory, But it is showing error and it not
> > converted into pdb.
> > Please suggest me my error.
> >
> > Thanks
> > Hirdesh
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Mon Feb 07 2011 - 21:30:04 PST
