[AMBER] Could not find vdW (or other) parameters for type: Na+

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Thu, 18 May 2017 11:13:40 +0000

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,


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Received on Thu May 18 2017 - 04:30:02 PDT
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