Dear AMBER users,
I am trying to build-up the prmtop and inpcrd files for the ligand solvated
structure for the QMMM calculation. Actually, I built-up the prmtop and
inpcrd files for my ligand-solvated structure using opc3pol water model.
ran till equilibration, Now for the production run, sourced tip3p water
model ff and now want to generate the prmtop and inpcrd files using this
tip3p water model. But, it seems lig-solv.prmtop and inpcrd files not
correctly generated.
I have used this:
*source /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/cmd/source
leaprc.water.tip3psource leaprc.gaff2loadamberparams pyrrole.frcmodligand
=loadmol2 pyrrole.mol2check ligandmol =loadpdb lig-solv.pdb (which was used
before using opc3pol water model)setbox mol vdwsaveamberparm ligand
lig-solv-qmmm.prmtop lig-solv-qmmm.inpcrdquit*
Kindly suggest me how can I generate correctly the prmtop and inpcrd files
for ligand solavted structure ?
Thanks & Regards
Kankana Bhattacharjee
Ph.D. Scholar
Department of Chemistry
Ashoka University
Sonipat, Haryana
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Received on Thu Jan 09 2025 - 11:00:02 PST
