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

From: Thakur, Abhishek <>
Date: Mon, 15 May 2017 16:01:42 +0000

Hi Dr.Case,

I have tried using NA and CL for sodium and chlorine but still similar error persist.

FATAL: Atom .R<CL 545>.A<CL 2> does not have a type.
FATAL: Atom .R<NA 546>.A<NA 3> does not have a type.
FATAL: Atom .R<NA 547>.A<NA 3> does not have a type.

Thanking you,


From: David A Case <>
Sent: Friday, May 12, 2017 1:33:34 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 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
> quit

OK: you are rolling your own commands, and are pretty much on your own
to see what is going wrong. Consider using standard leaprc files (e.g.
leaprc.protein.ff14SB, leaprc.water.tip3p).

I note that you called chloride "Cl" in the loadmol2 command, but called
it "Cl-" in the addIons command. Look carefully at the leap.log file to
see exactly what is going on.

Here's my best guess: you get the error for "Na" because the Amber libraries
recognize "NA" and "Na+" (for backward compatibility), but don't have any
entries for "Na". There was no error for chloride because of the above typo
in the addIons command. Easiest fix is probably to edit your pdb file
and use "NA" and "CL" for sodium and chloride ions.


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