Hello all,
I’m working on a system consisting of a transporter protein with a ligand
positioned at a binding pocket and the whole system embedded in a lipid
bilayer. The bilipid layer was constructed using packmol-memgen. Before
that, I used Antechamber for ligand parameterization with the following
script:
*antechamber -i ligand.mol2 -fi mol2 -o UNL.mol2 -fo mol2 -c abcg2 -s 2 -pf
y -j 5 -at gaff2 -nc 0 antechamber -i UNL.mol2 -fi mol2 -o UNL.prep -fo
prepi -c abcg2 -s 2 -pf y -j 5 -at gaff2 -nc 0 parmchk2 -i UNL.prep -f
prepi -o UNL.frcmod -s 2*
During equilibration, with gradually decreasing positional restraints (~100
ns), the system remains stable. However, once restraints are fully lifted
in the production run, the ligand instantly dissociates and flies away.
Initially, I had used -j 4, but some double bonds were incorrectly assigned
during parametrization, so I switched to -j 5 as it allows to read the
connectivity table from the input and then run ’bondtype’ and ’atomtype’
sequentially. My current guess is that the issue lies in ligand
parametrization—possibly incorrect charges or missing parameters. I don't
see issues after running parmchk2, however. Any suggestions or insights
would be appreciated.
*Pitambar Poudel*
Graduate Research Assistant
Computational Biophysics and Bioinformatics Lab
Department of Physics and Astronomy, Clemson University
*Lab: http:/compbio.clemson.edu/ <http://compbio.clemson.edu/lab/>*
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Received on Thu Jun 19 2025 - 14:30:02 PDT
