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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- application/octet-stream attachment: tleap.in
- application/octet-stream attachment: sej.ac
Received on Mon Sep 09 2024 - 11:30:02 PDT
