On Fri, Apr 15, 2016 at 8:16 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
> Dear Sir,
>
> Thanks for your reply. The problem is at charmmlipid2amber step and the
> output file was not generated for the following command.
>
> $ charmmlipid2amber.py –i rec.pdb [-c substitution_definitions.csv] \ -o
> rec2.pdb
>
This seems like a danger of blind copy-and-paste. The \ character is
there to allow you to continue a command on the next line (it does this by
"escaping" the newline). If you put everything on the same line, you
should not use the \.
But that's not the problem. The problem here is that you copied the [-c
substitution_definitions.csv]. The brackets there are to indicate that
this argument is optional, but there is a default provided. So take that
stuff out and try the command again.
charmmlipid2amber.py -i rec.pdb -o rec2.pdb
You should inspect every command that you run and make sure you understand
what everything is doing.
HTH,
Jason
--
Jason M. Swails
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Received on Fri Apr 15 2016 - 13:30:04 PDT
