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

From: Kenneth Huang <>
Date: Fri, 12 Feb 2021 17:32:32 -0500


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" }}

I think most of that is already be in leaprc.DNA (not sure about the O01,
etc, but check leaprc). Does it give you any indicators of what atom
types/names don't have types? It's might be a name mismatch, since you're
loading in a couple other things. I'd check the output of leap.log right

mol=loadpdb 4wlw_AB_NTA.pdb

Since it should tell you what's missing/wrong/etc



On Fri, Feb 12, 2021 at 2:09 PM Alysia Mandato <>

> 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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