Hi Justin and all
when I do this command: pdb2gmx -ignh -f .pdb -o .pdb -water spce
with OPLS force field.
it seems that the protein has the charge of -3, while the ligand has the
charge of 0.890 and finally it prints that the final charge is -2.11. I
neutralized this charge with 2 NA+ so -0.11 charge remain (sorry for my
mistake this is 0.11 not 0.08).
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 3653, now 3653
Generating angles, dihedrals and pairs...
Before cleaning: 9612 pairs
Before cleaning: 9677 dihedrals
Keeping all generated dihedrals
There are 9677 dihedrals, 699 impropers, 6622 angles
9552 pairs, 3653 bonds and 0 virtual sites
Total mass 25805.536 a.m.u.
Total charge -3.000 e
Writing topology
Back Off! I just backed up posre_A.itp to ./#posre_A.itp.2#
Processing chain 2 'R' (12 atoms, 1 residues)
Checking for duplicate atoms....
Now there are 11 atoms. Deleted 1 duplicates.
Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat
6 out of 6 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
Now there are 1 residues with 27 atoms
Chain time...
Back Off! I just backed up topol_R.itp to ./#topol_R.itp.2#
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 26, now 26
Generating angles, dihedrals and pairs...
Before cleaning: 60 pairs
Before cleaning: 60 dihedrals
Keeping all generated dihedrals
There are 60 dihedrals, 5 impropers, 45 angles
60 pairs, 26 bonds and 0 virtual sites
Total mass 175.212 a.m.u.
Total charge 0.890 e
Writing topology
Back Off! I just backed up posre_R.itp to ./#posre_R.itp.2#
Including chain 1 in system: 3623 atoms 226 residues
Including chain 2 in system: 27 atoms 1 residues
Now there are 3650 atoms and 227 residues
Total mass in system 25980.748 a.m.u.
Total charge in system -2.110 e
What should I do to my ligand charge in order to have complete charge?
thanks
--
Tehran University of Medical Sciences
www.tums.ac.ir
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