Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na

From: Thakur, Abhishek <>
Date: Thu, 11 May 2017 21:37:54 +0000

Hi Dr. Case,

I have been doing

tleap -s -f leaprc.ff14SB.ORIG
source leaprc.gaff
loadamberparams UNK.frcmod
loadoff UNK.lib
Na = loadmol2 Na.mol2
Cl = loadmol2 Cl.mol2
R_config = loadpdb C8_2.pdb
solvateBox R_config TIP3PBOX 10
charge R_config
addIons R_config Cl- 2
loadAmberParams frcmod.ionsjc_tip3p
saveamberparm R_config C8.prmtop C8.inpcrd
savepdb R_config complex.pdb

From: David A Case <>
Sent: Thursday, May 11, 2017 8:02:00 AM
To: AMBER Mailing List
Subject: Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na

On Thu, May 11, 2017, Thakur, Abhishek wrote:
> I have two sodium and one chlorine ions positioned at a specific
> position in my complex structure.
> So for this complex when I am trying to make prmtop and inpcrd file I am
> getting an error for my sodium ions.
> For atom: .R<Na 600>.A<Na 1> Could not find vdW (or other) parameters
> for type: Na

You should tell us what commands you gave to tleap, that is, which parameters
(usually via leaprc files) you loaded.

However, the correct atom and residue name for sodium ions is "NA" (for both
the atom and the residue). This is the PDB standard, which we try to
follow. For backwards compatibility, I think tleap still recognizes "Na+",
but that is an Amber-ism and should be discouraged.

The correct atom/residue name for chloride is "CL". There is not enough
information in your email to determine how that is being processed. You
can always use the "desc" command in tleap to see what residues are loaded.

....hope this helps....dac

AMBER mailing list
AMBER mailing list
Received on Thu May 11 2017 - 15:00:02 PDT
Custom Search