I am doing DNA ligand complex studies using Gromacs. I have use Amber sb ildn forcefield and make topology file for ligand using Acpype. It shows error that the solv.gro file and topol.top file have different atoms. i have used the following commands
grep 'ATOM ' complex.pdb>| DNA.pdb
grep 'HETATM ' complex.pdb>| ligand.pdb
gmx pdb2gmx -f DNA.pdb -o DNA.gro -water spc -ignh -v -p topol.top
Add H to ligand through pymol
conda activate AmberTools21
antechamber -i Ligand.pdb -o Ligand.mol2 -fi pdb -fo mol2 -c gas
python acpype.py -i Ligand.mol2
Merge DNA.pdb + updated Ligand_NEW.pdb -> Complex.pdb
grep -h ATOM DNA.pdb Ligand.acpype/Ligand_NEW.pdb >| Complex.pdb
cp Ligand.acpype/Ligand_GMX.itp Ligand.itp
3. `#include "Ligand.itp"` has to be inserted right after
`#include "amber99sb.ff/forcefield.itp"`line and before `DNA_*.itp` line in _topol.top_.
cat topol.top | sed '/forcefield\.itp\"/a\
#include "Ligand.itp"
' >| topol.top
echo "Ligand 1" >> topol.top
# Setup the box and add water
gmx editconf -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0
gmx solvate -cp Complex.pdb -cs spc216.gro -o Complex_b4ion.pdb -p topol.top
Create ions.mdp file
cat | ions.mdp
Why you are not trying Desmond (Academic Free version) for Protein-DNA complex simulation.
Check your complex file. There could be an error in the calculating total number of atoms of the system.
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