I’d be grateful for suggestions regarding the problem I encountered trying to generate topologies of a solvated dimer. I got the following error message
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
Loading library: /Users/gtzotzos/Programs/amber14/dat/leap/lib/atomic_ions.lib
Did charge the dimer
charge DIMER
Total unperturbed charge: -17.996999
Total perturbed charge: -17.996999
> addions DIMER Na+ 0
Added ions
addions DIMER Na+ 0
18 Na+ ions required to neutralize.
Using default radius 1.50 for ion Na+
Adding 18 counter ions to "DIMER" using 1A grid ….etc
Solvated the dimer
solvateoct DIMER TIP3PBOX 9.0
(using default radius 1.500000 for Na+)
(using default radius 1.500000 for Na+) ….etc
Volume: 465571.377 A^3 (oct)
Mass > 251520.908 amu, Density > 0.897 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 12324 residues.
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Received on Tue Aug 08 2017 - 11:00:02 PDT
