AMBER Archive (2004)

Subject: AMBER: An question about PTRAJ

Date: Fri Sep 10 2004 - 20:29:17 CDT

Dear sir
        My name is Morris. I wet a problem when I was using the IMAGE function
of the PTRAJ.
        Due to the periodic box condition, my DNA and its bindtion protein were
seperated visually. For my analysis, I tried to used the PTRAJ to put them
together. According the instruction, I use the IMAGE. But I can't solve the
The commands which I had used are listed bleow:
1, image origin, I got single strand back. The other one is still in the other
side of the box.
2, image center bymask :195-218, no function.
3, image center:195-218 bymask :195-218, still no function
the 195-218 is the residue number of DNA double helix

If you have similiar experience, please let me know your solution. I'll
appreciate it.

Y. Morris Chen

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