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#37189 - 11/13/18 05:21 AM Flipping a protein segment with com at origin
vidhya Offline
Forum Member

Registered: 08/09/18
Posts: 11
Loc: India
Hi

I am carrying out simulations using two protein segments. I wish to flip one segment 180 degrees with respect to the other so that the N and C termini of the two segments are oriented in opposite fashion.

I tried using COOR ROTA AXIS PHI 180 SELE SEGID P2 END

But this command not only flips the segment by 180 degrees but also moves the segments away from each other outside the water box.
How can I just flip the segment without translating them along an axis?

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#37190 - 11/13/18 11:54 AM Re: Flipping a protein segment with com at origin [Re: vidhya]
rmv Online   content

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Registered: 09/17/03
Posts: 8336
Loc: 39 03 48 N, 77 06 54 W
The result of the above command depends on how you defined the axis via the COOR AXIS command. If you want to rotate around e.g. the lab frame x axis, replace AXIS with XDIR 1.0, which defines a unit vector along the x axis.
_________________________
Rick Venable
computational chemist


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