Just a follow up explanation...
The problem is that H++ protonates HIS residues (and maybe ASP/GLU/LYS) without changing their names to fit the AMBER's convention (HIE, HID, HIP, ASH, GLH, LYH). By default tleap interprets HIS as HIE (the most common protonation state, see any leaprc.protein.*), then the conflict arises at the level of the residue library cause there are unexpected atoms in those residues...
Renaming HIS to the proper name is the solution...
Other way to get a proper protonation is by using PDB2PRQ server [
http://nbcr-222.ucsd.edu/pdb2pqr] which allows you to chose the output naming convention (e.g. AMBER).
Best
Matias
----- Mensaje original -----
De: "Matias Machado" <mmachado.pasteur.edu.uy>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Sábado, 10 de Agosto 2019 16:39:12
Asunto: Re: [AMBER] T-leap "does not have a type"
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".
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Parviz Seifpanahi Shabane" <sparviz.vt.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
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++ (
http://biophysics.cs.vt.edu/) 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
WAT=OPC
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.top 1KX5-ED25A-HPP-PDB-iodFF.crd
quit
Best
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Sat Aug 10 2019 - 13:30:02 PDT
