[AMBER] changing X Y Z orientation

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Fri, 18 Mar 2011 10:47:21 +0000 (GMT)

Dear Sir/ madam,

I have a problem to be solved.
Basically, I am simulating bilayer system.
The arrangement of lipids in bilayers are as bellow:

| | | | |
| | | | |

| | | | |
| | | | |

------> X direction

Normally, by conventional way, the long vertical axis shall be Z, horizontal axis shall be X and Y respectively.

I have several bilayers systems like this but all are not the same as conventional format as I mentioned above.

For some systems the long vertical axis become Y and the other two horizontal axis become Y and Z. This I think could be the reason using hyperchem to model the system.

This actually giving me problem now to select certain layer specifically during analysis.

I just curious to know is there any way by using PTRAJ or other tools to convert the problematic system as the conventional format?

I really appreciate any help. many thanks in advance.


Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,


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Received on Fri Mar 18 2011 - 04:00:03 PDT
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