Thanks a lot for your time. I am a fresh man and I am just trying to learn amber! since I really need it. :(
I have gotten this command from here:
http://ambermd.org/tutorials/basic/tutorial3/section1.htm
and unfortunately, I have the same problems with commands in the Amber 15 manual and this site "
http://ambermd.org/tutorials/basic/tutorial1/section2.htm". I could not simulate the duplex DNA with the command:
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
I encounter this error, -bash: syntax error near unexpected token `('
would you please tell me the reason behind this error and in addition, I really appreciate it if you could provide me with an up to dated manual or site, so I could work with Amber tools15.
Best regards,
Mahdieh
________________________________________
From: David A Case [david.case.rutgers.edu]
Sent: Monday, February 22, 2016 8:53 PM
To: AMBER Mailing List
Subject: Re: [AMBER] No exe file in Amberhome
On Mon, Feb 22, 2016, Mahdieh Hadi wrote:
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99
> I encounter the following error:
>
> -bash: /Users/amber14/exe/xleap: No such file or directory
Correct. Not sure where the above line came from. You can either type:
$AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99
^^^^^
or (since xleap is probably in your PATH):
xleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99
Notes:
1. You probably got your sample command from some old source, since (many
years ago) Amber executables were put in the $AMBERHOME/exe directory, instead
of $AMBERHOME/bin. But that has not been true for a long time.
2. Also related to old files: the "olff" part of your command means "old force
field", and leaprc.ff99 is very, very much out of date. Unless you are *sure*
you know what you are doing, try this: 'xleap -f leaprc.ff14SB'
3. If you point us to where you got the confusing command from, we'll fix it.
...thanks...dac
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Received on Mon Feb 22 2016 - 13:00:04 PST
