On Tue, Aug 08, 2017, George Tzotzos wrote:
>
> saveamberparm DIMER complex_solv.prmtop complex_solv.inpcrd
>
> Checking Unit.
> Building topology.
> Building atom parameters.
> For atom: .R<Na+ 254>.A<Na+ 1> Could not find vdW (or other) parameters for type: Na+
> For atom: .R<Na+ 255>.A<Na+ 1> Could not find vdW (or other) parameters for type: Na+
> ……………………………………………………………………………etc
> For atom: .R<Na+ 271>.A<Na+ 1> Could not find vdW (or other) parameters for type: Na+
> Parameter file was not saved.
>
> Can’t figure this out as I did source leaprc.ff14SB
But you never loaded the parameters for the ions. In old versions of Amber,
you must use loadAmberParams to choose the force field parameters for the ions
that go along with your chosen water model.
I strongly recommend upgrading to AmberTools17 (although the relevant changes
were also present in AmberTools16 -- we haven't supported a "leaprc.ff14SB"
in either of the past two releases.)
With AmberTools17, there are leaprc.protein.*, leaprc.DNA.*, leaprc.RNA.*
and leaprc.water.* files. By choosing a water model, you automatically get
the corresponding ion files that go with that water model.
A couple notes:
1. you can keep pmemd from Amber14 and still use everything else from
AmberTools17. (pmemd is the only program not in AmberTools). Just set
your AMBERHOME variable to the amber16 tree: the pmemd program doesn't need
or use the AMBERHOME variable. (Of course, you can also upgrade to Amber16
if you wish.)
2. Going forward, use "NA" for sodium, not "Na+". The former is the PDB
standard; the latter is a non-standard name that should be phased out.
....dac
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Received on Tue Aug 08 2017 - 13:00:02 PDT
