hello,
After your last command, write: go. Thus, the program will begin to work and to
write your output file.
Pascal
On Oct 9, 5:16am, ZhiYong Zhang wrote:
> Subject: One question about praj
> 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
> ********************************************************
>-- End of excerpt from ZhiYong Zhang
--
********************************************************************************
Pascal Bonnet pascal_at_qorws1.uab.es
Unitat Quimica Organica and Institut de Chimie Organique et Analytique
Facultat de Ciences UFR Sciences - UMR 6005
Universitat Autonoma de Barcelona Rue de Chartres - BP 6759
08193 Bellaterra (SPAIN) 45067 ORLEANS CEDEX 2 - France
Tel: 34935811266 Tel: 0238494577
Fax: 34935811265
********************************************************************************
Received on Tue Dec 19 2000 - 09:32:32 PST
