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

[Viswanadham Sridhara]

Looks fine to me.
you can add 18 positive (Na) ions to neutralise.


On 10/19/06, "Stefan Schöbel" <s.schoebel1 at gmx.net> wrote:
>
> 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:
>                  CYS102
>                   SG760
> 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
> NOTE:
> 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
>
> Stefan
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-- 
Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.
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