Dear Amber experts,
I have AMBER16 and AMBER Tools16
I am trying to apply MM-PBSA algorithm
for my protein-protein complex.
One protein contains chelating Na+ ion.
The latter circumstance causes the reporting
error message:
Building topology.
Building atom parameters.
For atom: .R<NA 743>.A<NA 1> Could not find vdW (or other) parameters for type: Na+
Parameter file was not saved.
when I used the TLEAP procedure for files preparation:
tleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff14SB
h = loadpdb h_rep_c0_fr_75761_nh.pdb
set default PBRadii mbondi2
saveamberparm hht h.prmtop h.inpcrd
What command line should be added to TLEAP to account for
vdW radii for chelating Na+ and resolve the problem?
Thank you,
Michael
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Received on Thu May 18 2017 - 04:30:02 PDT
