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

From: Alysia Mandato <alysiamandato.gmail.com>
Date: Fri, 12 Feb 2021 14:08:52 -0500

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
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Received on Fri Feb 12 2021 - 11:30:02 PST
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