On Thu, Jun 30, 2016, James Starlight wrote:
> source leaprc.ff03.r1
> source leaprc.gaff
> FATAL: Atom .R<CU 898>.A<CU 1> does not have a type.
> FATAL: Atom .R<MG 899>.A<MG 1> does not have a type.
> FATAL: Atom .R<CA 900>.A<CA 1> does not have a type.
> FATAL: Atom .R<CU 901>.A<CU 1> does not have a type.
> FATAL: Atom .R<CU 902>.A<CU 1> does not have a type.
You are not loading any parameters for ions with charge greater than +1.
You can look at the "Ions" section in the Reference manual for details
about how to do this.
I would strongly recommend upgrading to AmberTools16, since we have greatly
simplified the handling of ions. Now, you choose a water model (say tip3p),
and load leaprc.water.tip3p into tleap. This automatically loads the water
parameters and corresponding monatomic ion parameters for a large number of
ions. You can read about what is done in the "Ions" section of the new
Reference Manual.
...dac
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Received on Thu Jun 30 2016 - 05:30:05 PDT
