Hi,
It seems you have not loaded the parameters for Na+ ions
You can load them by this command in leap
loadamberparams frcmod.ionsjc_tip3p
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Michael Shokhen [mailto:michael.shokhen.biu.ac.il]
Sent: Thursday, May 18, 2017 4:44 PM
To: AMBER.ambermd.org
Subject: [AMBER] Could not find vdW (or other) parameters for type: Na+
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 - 06:00:03 PDT
