Thanks so much for the help!
Yes defenetely the ions are coordinated with the protein - I will try
to switch to amber-tools 16 and report my progress after.
Regards,
James
2016-06-30 14:13 GMT+02:00 David A Case <david.case.rutgers.edu>:
> 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 - 06:30:03 PDT
