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 Fri Aug 17 2018 - 06:30:06 PDT
