[gmx-users] system net charge 0f -1.6

"Stefan Schöbel" s.schoebel1 at gmx.net
Fri Oct 20 03:30:33 CEST 2006

I am using only a protein and the GROMOS96 43a1 force field. 
After pdb2gmx I got:
Back Off! I just backed up test.top to ./#test.top.3#
Processing chain 1 (1594 atoms, 214 residues)
There are 288 donors and 315 acceptors
There are 479 hydrogen bonds
Will use HISB for residue 45
Will use HISB for residue 79
Will use HISB for residue 177
Will use HISB for residue 202
Checking for duplicate atoms....
Now there are 1593 atoms. Deleted 1 duplicates.
Opening library file /home/mpaetzel/programs/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
  CYS167  SG1251   2.930
N-terminus: NH3+
C-terminus: COO-
Now there are 214 residues with 1957 atoms
Making bonds...
Opening library file /home/mpaetzel/programs/share/gromacs/top/aminoacids.dat
Number of bonds was 1996, now 1991
Generating angles, dihedrals and pairs...
Before cleaning: 3360 pairs
Before cleaning: 3782 dihedrals
There are 1101 dihedrals,  946 impropers, 2896 angles
          3360 pairs,     1991 bonds and     0 virtual sites
Total mass 22620.601 a.m.u.
Total charge -18.000 e
Writing topology

--> why are the HIS residues changed into HISB?

after editconf:

Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 7683
Excluding 2 bonded neighbours for SOL 2730
  System has non-zero total charge: -1.800000e+01

I tried adding C term Oxygen with spdbv as well, but it still the same uneven charge.

What happened?

thanks in advance 

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