AMBER: Understading of mdcrd file and pdb file..

From: Vijay Manickam Achari <>
Date: Fri, 16 Nov 2007 05:02:08 +0000 (GMT)

Dear Amber users,

>From MD coordinate file, xxxx.mdcrd, I have generated
xxxx.pdb files using ptraj program.

In one nanosecond simulation, I can generate 1000
frames of pdb file from MD coordinate file.

The question is, how the X,Y,Z coordinates from pdb
file written in coordinate file? I dont understand the
sequence how the coordinates are arranged in mdcrd
file and pdb file.

I am trying to extract some information from mdcrd
file. So I need to know the sequence how the X,Y,Z
coordinates are arranged in mdcrd file accordance with
pdb file.

Can anyone help me to explain how the arrangement is?

Thank you in advance.

Vijay Manickam Achari
Phd Student
University Malaya,

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Received on Sun Nov 18 2007 - 06:07:40 PST
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