Re: [AMBER] tLeap, Fatal: Atom does not have a type

From: Maria Nagan <>
Date: Fri, 12 Feb 2021 17:41:58 -0500


Kenneth is right - you have weird atoms. What are O01, O02 and O03 representing?

Do you have an extra protonated phosphate? That might be your problem. You need your DNA residues to match the lib file you gave it (parmBSC1.lib). So you need parameters for a residue with an extra phosphate.

I’m not sure why you add PO1. What is that? Is it an O5’ or O3’?

Remember that the only atom types allowed are the ones you define with your leaprc files (found in $AMBERHOME/dat/leap/lib/parmBSC1.lib according to your leaprc.DNA.bsc1).

You shouldn’t have to add atom types P, OP1, OP2. These are standard in parmBSC1.lib.


> On Feb 12, 2021, at 2:08 PM, Alysia Mandato <> wrote:
> Hello all,
> I am solvating a protein-DNA system with a few modifications. I know these
> modification steps work, but I am running into a fatal error when I check
> my pdb. I'm having a lot of trouble solving this fatal error in my tleap
> script. When I "check mol", I have fatal errors saying that I have atoms
> that do not have a type. I tried using the addAtomTypes command, and I am
> not sure I am doing it properly. Any guidance would be greatly appreciated.
> These are the steps I am using:
> source leaprc.protein.ff14SB
> source leaprc.DNA.bsc1
> source leaprc.water.tip3p
> addAtomTypes {{ "P" "P" "sp3" }{ "OP1" "O" "sp2" }{ "OP2" "O" "sp2" }{ "PO1
> "P" "sp3" }{ "O01" "O" "sp2" }{ "O02" "O" "sp2" }{ "O03" "O" "sp2" }{ "HO1"
> "H" "sp3" }{ "HO2" "H" "sp3" }}
> loadamberprep HIC.prepi
> loadamberprep NTA.prepi
> loadamberparams HIC.frcmod2
> loadamberparams NTA.frcmod2
> mol=loadpdb 4wlw_AB_NTA.pdb
> bond mol.60.CA mol.333.C13 S
> bond mol.64.CA mol.333.C12 S
> bond mol.196.CA mol.334.C13 S
> bond mol.200.CA mol.334.C12 S
> solvateoct mol TIP3PBOX 15.0
> addions mol Cl- 228
> addions mol Na+ 228
> savepdb mol 4wlw_nta_solv_bonds.pdb
> check mol
> saveamberparm mol 4wlw_nta.prmtop 4wlw_nta.prmcrd
> quit
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Received on Fri Feb 12 2021 - 15:00:03 PST
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