Re: [AMBER] T-leap "does not have a type"

From: Matias Machado <>
Date: Sat, 10 Aug 2019 16:39:12 -0300 (UYT)

Dear Parviz Seifpanahi Shabane,

HIE is a Histidine protonated at N epsilon, hence AMBER expect to find HE2 instead of HD1 (Histidine protonated at N delta, HID)... you are having a residue name conflict with the library "amino12.lib".



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Parviz Seifpanahi Shabane" <>
Para: "AMBER Mailing List" <>
Enviados: Viernes, 9 de Agosto 2019 13:47:14
Asunto: [AMBER] T-leap "does not have a type"

Hi All,
I protonated my PDB file (1KX5) by H++ ( at
Ph= 7.5. When I am running T-leap by using the PDB created from H++, the I
am getting this error message R<HIE 1178>.A<HD1 18> does not have a type.
I want to keep the system at Ph=7.5 and not changing anything. How can I
solve this?
this mt T-leap script:
source /usr/local/amber18/dat/leap/cmd/oldff/leaprc.ff99SB

set default PBradii bondi
mods = loadAmberParams frcmod.opc
mods = loadAmberParams frcmod.ions1lm_126_iod_opc
mol = loadpdb 1kx5-HPP.pdb
#addions mol Na+ 0
#addions mol Cl- 0

solvateBox mol OPCBOX 25

#addions mol Na+ 0
#addions mol Cl- 0

saveamberparm mol 1KX5-ED25A-HPP-PDB-iodFF.crd

Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Sat Aug 10 2019 - 13:00:01 PDT
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