I want to perform molecular dynamics of protein-ligand complex simulations by amber force field. but my ligand conatins 3 protonated amine. so can help me how to make the topology and parameter files?
Thanks. Regards
Ho Sourav,
Try Open Babel to protonate your ligands.
babel -imol2 ligand.mol2 -omol2 ligand_H.mol2 -p 7.0
In antechamber, you should add "-nc +1".
Thank you...bt I did topology generation in antechamber as same way ..bt after that during energy minimization it's showing error during charge clash...
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Running: /home/arindam/miniconda3/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Info: Bond types are assigned for valence state (1) with penalty (1).
Running: /home/arindam/miniconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 273; net charge: 0
Info: The number of electrons is odd (273).
Please check the total charge (-nc flag) and spin multiplicity (-m flag).
Running: /home/arindam/miniconda3/bin/sqm -O -i sqm.in -o sqm.out
/home/arindam/miniconda3/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/home/arindam/miniconda3/bin/sqm -O -i sqm.in -o sqm.out".
this error come when -nc was not used
but after -nc command used in antechamber the program has been run bt when the energy minimization is going on then the following error come:
"Water molecule starting at atom 69515 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate."
where is the problem?
bt when there is no protonated ligand then the energy minimization is smoothly going on
I am unable to generate parameter for iodide ion in tleap of amber. Amber parameter database doesn't have parameter for it. The force field I am using is ff99SB. Kindly suggest how I can go about it? Sourav Pal Yoshinobu Ishikawa Bryan Moloto Anwesh Pandey
Hi Subhanjan,
You should also source leaprc.water.tip3p in tleap.
I am very new in computational chemistry.Can you suggest any reference regarding manual parametrization of monovalent ion? How to do it with iodide ion? Anwesh Pandey
Yoshinobu Ishikawa