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

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Thu, 18 May 2017 12:56:25 +0000

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
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