Hi, Thomas
Thanks for your quick replay
The center command indeed put the first residue on origo,
but the image command did not fix the "look" of the water molecules.
Some of the waters are still at a distance.
/ Samuel
2010/6/14 Thomas Cheatham <tec3.utah.edu>:
>
>> We have had much problems with wrapping with ptraj.
>> Here is an example, where we try to centre on the first atom and wrap
>> into an octahedral box, but we get a number of waters at a distance and
>> therefore also a wrong centering.
>
> I believe you want to center about residue #1 and then image. Your script
> was:
>
> trajin m1
> trajout pdb pdb
> image origin center familiar com :1
>
> What you want is:
>
> trajin m1
> trajout pdb pdb
> center :1 mass origin
> image origin center familiar
>
> --tec3
>
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Received on Mon Jun 14 2010 - 04:00:06 PDT
