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

[Tsjerk Wassenaar]

Hi,

Actually, the decision between HISA and HISB is made based upon some
criteria, which use the environment of the histidine residue. As
mentioned, you can manually set the type using the -his flag

Best,

Tsjerk

On 10/20/06, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
> Hi,
>
> On Friday 20 October 2006 03:30, Stefan Schöbel 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?
>
> you can change this interactivly with pdb2gmx. Option is -his (and others)
>
> >
> > 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
>
> Florian
>
> --
> -------------------------------------------------------------------------------
>  Florian Haberl
>  Computer-Chemie-Centrum
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Telephone:     +49(0) − 9131 − 85 26581
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------------
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336