AMBER Archive (2000)

Subject: One question about praj

From: ZhiYong Zhang (zzy_at_mail.ustc.edu.cn)
Date: Mon Dec 18 2000 - 21:59:14 CST

Dear Amber users,
        I just began to learn how to use Amber 6. I want to Use ptraj Cut
down a cubic box to a truncated octahedral shape. So, I type following
command lines according to manual:

1)ptraj spepcubetop.wat
PTRAJ: Processing input file...
       Input is from standard input

2)trajin spepcubecrd.wat
PTRAJ: trajin spepcubecrd.wat

3)trajout spepoctcrd.wat
PTRAJ: trajout spepoctcrd.wat

4)truncoct :1-15 10.0 prmtop spepocttop.wat
PTRAJ: truncoct :1-15 10.0 prmtop spepocttop.wat
Mask [:1-15] represents 229 atoms

        According to the output, I cannot know if these commands are run
correctly? Furthermore, I do not know how to exit ptraj (q or quit?) and I
found that output file did not produced. Would anyone give me a hand? Thanks in
advance.

Zhiyong

*********************************************************
Zhiyong Zhang, Ph.D student of Professor Yunyu Shi,
Laboratory of Structural Biology,
School of Life Science,
University of Science and Technology of China (USTC),
Hefei, Anhui 230027,
P.R. China.
Tel: +86-551-3603754 or +86-551-3630875
Fax: +86-551-3603754
Email: zzy_at_mail.ustc.edu.cn
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