AMBER Archive (2006)

Subject: Re: AMBER: respin file

From: M. L. Dodson (mldodson_at_houston.rr.com)
Date: Sat Nov 25 2006 - 08:37:05 CST

On Saturday 25 November 2006 01:06, Fenghui Fan wrote:
> Dear all,
>
> I have the following ac file:
>
> ----------------
> --Link1--
> %chk=molecule
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2)
> iop(6/42=6) opt
>
> remark line goes here
>
> 1 1
> N -1.5610 -6.3170 13.8420
> H -1.1260 -7.1890 13.5780
> C -1.2580 -5.7560 15.1880
> H -2.1820 -5.5360 15.7030
> C -0.4500 -6.7740 15.9970
> H 0.3770 -7.1300 15.4040
> H -1.0860 -7.6050 16.2650
> S 0.1800 -5.9910 17.5030
> C -0.4460 -4.4700 15.0230
> O 0.6070 -4.4640 14.4180
> Zn 1.5170 -7.5220 18.5860
>
> ---------------
>
> ANd I use the following command to get the respin
> file:
> ------------------
> nohup $AMBERHOME/exe/respgen -i input.ac -o 1.respin1
> -f resp1
> ------------------------
>
> Then I use the following command to get the respout
> file"
>
> ------------
>
> nohup $AMBERHOME/exe/resp -o -i 1.respin1 -o
> fenghui.respout1 -e sustiva.esp -t qout_stage1
> ----------------------
>
> But the following message occurs:
>
> -------------------------
> Amber 9 RESP
>
>
> unknown flag: 1.respin1
>
>
>
>
> usage: resp [-O] -i input -o output -p punch -q qin
> -t qout -e espot -w qwts -s esout
>
> -------------------------
>
> Will you please tell me why 1.respin1 is a unknown
> flag?
>
> I am looking forward to getting your reply.
>
> Best regards.
>
> Fenghui Fan
>

Follow along with the following analysis.

I copied your input line here (I assume that this was all on one
line when you typed it in):

nohup $AMBERHOME/exe/resp -o -i 1.respin1 -o
fenghui.respout1 -e sustiva.esp -t qout_stage1

I copied the command line in the usage error message here (again
this should be all on one line):

usage: resp [-O] -i input -o output -p punch -q qin
-t qout -e espot -w qwts -s esout

Compare the two carefully. Your command line contains the string

-o -i 1.respin1

Now what does this mean? -o means that the following string on
the command line is the output file name, so the output file name
requested is "-i". What is left in our string after the "-o
output" (which is required; look at the usage string) is parsed?
"1.respin1". Look at the usage example. All options require a
flag indicating their meaning be the first thing the parser
encounters for each option. There is no allowance for a bare
string with no accompanying flag (flags are things starting with
"-") preceeding it. So the parser interprets "1.respin1" as a
flag. The program does not know what to do with a flag equal to
"1.respin1". That is what the error message is telling you.

I'm sorry if this explanation sounds condescending, but this
analysis was truly trivial. If you are going to be successful
with the amber suite of tools, you have to be able to do this kind
of analysis and input debugging on your own without asking the
list. The people on this list are busy, and do not have time to
answer these kinds of trivial questions. Even though they are
busy, the amber list is among the most responsive technical
support lists to which I have ever subscribed. The lesson here is
to try very hard to solve your problems on your own by reading the
manual, consulting the tutorials and list archives, searching the
internet (Google is your friend), etc. Then ask the list if you
are still unable to solve your problem.

I apologize in advance to the readers of the list. This is my
answer and mine alone, and should not reflect negatively on the
list members as a whole.

Bud Dodson 

-- 
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-56_three-386_one

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