Hello David,
Thank you for your advice.
It partially worked which is very helpful.
So I am able to successfully load tleap and run it.
But my variables do not transfer across from the bash line to tleap
I use
*NAME=$1CHARGE=$2GPU=$3export NAME export CHARGEexport GPU*
*tleap -f tleap*
The second script is called tleap but the variable dont come across into
the second script
On Fri, 17 Aug 2018 at 14:29, David A Case <david.case.rutgers.edu> wrote:
> On Fri, Aug 17, 2018, Keiran Corbett wrote:
>
> > So I need to run a number of calculations on 200 Lig/proteins so am
> trying
> > to write a script to automate the process a little more
> > I have two input files
> > *tleap -f leaprc.gaff -f leaprc.ff14SB -f tleap2.txt *
> > which then opens the file tleap2.txt
>
> As you note, the problem seems to be in the tleap2.txt file, but you
> didn't include that in your email (as far as I can see), so people on
> the list won't be able to help.
>
> Suggestions:
>
> 1. just put "source leaprc.gaff" and "source leaprc.ff14SB" at the top
> of tleap2.txt, and just us a single -f flag to tleap.
>
> 2. consider upgrading to AmberTools18: files like leaprc.ff14SB were
> removed back in 2016, and there lots of improvements and bugfixes that
> you are missing by using old codes.
>
> 3. consider using gaff2 rather than gaff (unless you have a particular
> need for the older version.)
>
> ...good luck...dac
>
>
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Received on Mon Aug 20 2018 - 02:30:02 PDT
