On Wed, Sep 05, 2012, Chris Chris wrote:
>
> xleap -s -f leaprc.ff10
You have to also explicitly load the ion set you want: ion parameters depend on
which water model you are using, and LEaP doesn't know in advance what that
is. Please see Section 2.11 in the AmberTools Reference Manual.
>
> This time my protein loaded with very few error messages
>
> Checking Unit.
> WARNING: There is a bond of 7.264594 angstroms between:
> ------- .R<SER 152>.A<C 10> and .R<GLU 153>.A<N 1>
> WARNING: There is a bond of 7.289787 angstroms between:
> ------- .R<SER 458>.A<C 10> and .R<GLU 459>.A<N 1>
You will need to address these problems...it is likely that there are missing
residues in the input PDB file, and you either have to generate initial
coordinates for them, or place TER cards to create separate chains.
> For atom: .R<Na+ 615>.A<Na+ 1> Could not find type: Na+
This will be fixed by loading the appropriate frcmod file for ions.
....dac
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Received on Wed Sep 05 2012 - 18:30:02 PDT
