Either the atom name or atom mass is not set correctly. The QM/MM interface uses these to deduce the atomic number.
You might want to check (using parmed) that the mass for this sulfur is correct. If not, set the mass for your atom type.
If the mass is correct, the issue could also be a missing addAtomTypes command. You can look at standard leaprc files to see examples. Add the corresponding addAtomTypes command to your prep file.
All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
On Sep 9, 2024, at 11:25 AM, SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <amber.ambermd.org> wrote:
Hi,
We are trying to perform QM/MM simulation for a complex PDB with covalent
bond between ligand and ser residue. We considered the Ser-ligand as a
modified amino acid (SEJ).
Following Antechamber, the atom type for a sulfur present in the ligand part
was given as "SO".
ATOM 12 SAR SEJ 2 -4.745 -3.032 57.169 1.710300 SO
While trying to run a QM/MM simulation, we got the following error in the
output file for minimization-
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: Atom number: 26 has atomic number -1.
QMMM: There are no PM3 parameters for this element. Sorry.
SANDER BOMB in subroutine qm2_load_params_and_allocate
UNSUPPORTED ELEMENT
QM PM3 NOT AVAILABLE FOR THIS ATOM
For Antechamber we have followed the AMBER Tutorial 2.3 Green Fluorescent
"""
antechamber -i SEJ_h_amb.pdb -fi pdb -fo ac -o sej.ac -c bcc -s 2 -at amber
-nc -1
prepgen -i sej.ac -o sej.prepin -m sej.mc -rn SEJ
parmchk2 -i sej.prepin -f prepi -o frcmod.sej -a Y -p
$AMBERHOME/dat/leap/parm/parm10.dat
grep -v "ATTN" frcmod.sej > frcmod1.sej
parmchk2 -i sej.prepin -f prepi -o frcmod2.sej
tleap -f tleap.in
Please find the attached files for reference.
Kindly help me in this regard.
Thank you
--
*Yours Sincerely*
*Subhasmita Mahapatra*
*Ph.D. Scholar (PMRF)*
*Computational Biophysics Group*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*Madhya Pradesh, India (453552)*
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Received on Mon Sep 09 2024 - 21:30:02 PDT
