Re: [AMBER] command from ambertools tutorial does not working

From: David A Case <>
Date: Wed, 27 Feb 2019 14:10:37 -0500

On Tue, Feb 26, 2019, Sasthi Charan Mandal wrote:

>It shows only syntax error.
>On Tue, Feb 26, 2019 at 11:12 PM Daniel Roe <> wrote:
>> What is the exact error message you receive?
>> > I am following the simulation of small fragment of DNA from
>> > ambertools tutorial. But I stuck on energy minimization step. the
>> > command : $AMBERHOME/bin/sander
>> > -O -i -o polyAT_vac_init_min.out -c
>> polyAT_vac.rst7
>> > -p polyAT_vac.prmtop -r polyAT_vac_init_min.ncrst is not working and it
>> > shows syntax error. Do I have to modify the command? could you please
>> help

We really need *exact* details, with a very strict interpretation of
the word "exact".

Did you type by hand the above command at the shell prompt? Was
everything on a single line? Can you copy and paste both what you typed
and the entire response that came to the terminal? Is there anything in
the " polyAT_vac_init_min.out" file?


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Received on Wed Feb 27 2019 - 11:30:02 PST
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