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 - 13:00:01 PDT
