Hi,
On Tue, Feb 8, 2011 at 12:23 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> 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*
I think what has happened here is your initial restart did not have
any velocity information (perhaps because it was generated with Leap?)
but the restart that ptraj generates has "placeholder" velocity info -
that is, all the velocities are set to 0.0 (doing a tail command on
the file should confirm this). It's not really a problem - just be
aware that the velocities in new.rst.1 are all at 0.0.
-Dan
>
> 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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>> >
>>
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Received on Tue Feb 08 2011 - 06:30:02 PST
