AMBER Archive (2005)

Subject: AMBER: average structure after MD

From: kuljeets_at_igib.res.in
Date: Wed May 25 2005 - 04:14:19 CDT

Dear friends,

I have performed a MD simulation and want to view the final average
strcture of the protein. Following is my avg.in file:

========================================
trajin umq_md2.mdcrd 33 38
center :22-81
image center familiar
rms first mass out av_rms_umq.dat :22-81
average umq_avg.pdb pdb
========================================

then I ran the ptraj..

When I saw the file umq_avg.pdb, I got the following:

ATOM 1 N LEU 1 ************************ 0.00 0.00
ATOM 2 H1 LEU 1 ************************ 0.00 0.00
ATOM 3 H2 LEU 1 ************************ 0.00 0.00
ATOM 4 H3 LEU 1 ************************ 0.00 0.00
ATOM 5 CA LEU 1 ************************ 0.00 0.00
ATOM 6 HA LEU 1 ************************ 0.00 0.00
ATOM 7 CB LEU 1 ************************ 0.00 0.00
ATOM 8 HB2 LEU 1 ************************ 0.00 0.00
ATOM 9 HB3 LEU 1 ************************ 0.00 0.00
ATOM 10 CG LEU 1 ************************ 0.00 0.00

........................and so on.

Although other things energy and rms plots are fine!
Where I am wrong??

Regards,
Kuljeet
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