It is working now.
Thank you!
Citiram Carlos Simmerling <carlos.simmerling.gmail.com>:
> do the center command first, then image.
>
>
> Hi
>>
>> I have some problems with ptraj option IMAGE and I would be very grateful
>> if someone could help me.
>> I have an enzyme and I am trying to put waters back in truncated octahedron
>> (I have made truncated octahedron using Leap and distance parameter of 7
>> angstroms). When I use:
>>
>> trajin mol-name.rst
>> image origin center familiar
>> center :1-11431 mass origin
>> trajout mol-nameOUT.crd
>>
>> I get water box with a shape of truncated octahedron but my enzyme is half
>> in and half out of that box. I do not know if I can use prtaj to put back
>> waters in truncated octahedron such that the closest distance between any
>> atom of the solute and the edge of the solute box is 7 angstroms (like
>> Leap). I do not know if this is possible or you can suggest me to do
>> something else.
>>
>> Gratefully
>> Antonija
>>
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>>
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Received on Mon Jul 06 2009 - 12:13:57 PDT
