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

From: Parviz Seifpanahi Shabane <sparviz.vt.edu>
Date: Fri, 9 Aug 2019 12:47:14 -0400

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 Fri Aug 09 2019 - 10:00:01 PDT
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