[gmx-users] (no subject)

[Jair]

Thank you. 
It works fine.


JJVC
jair at iq.ufrj.br

On Wednesday 20 October 2004 16:51, David wrote:
> On Wed, 2004-10-20 at 17:45, Andre Farias de Moura wrote:
> > On Wed, 20 Oct 2004, Jair wrote:
> > > Ok, I have tried this too, but make_ndx do not found the chains:
> > > *****
> > > Opening library file /chem/gromacs-3.2.1/share/top/aminoacids.dat
> > > There are: 15955   OTHER residues
> > > There are:  382  PROTEIN residues
> > > There are:   0    DNA residues
> > > Analysing Protein...
> > > Analysing Other...
> > >
> > >  0 System       : 54004 atoms
> > >  1 Protein       : 6155 atoms
> > >  2 Protein-H      : 3094 atoms
> > >  3 C-alpha       :  382 atoms
> > >  4 Backbone      : 1146 atoms
> > >  5 MainChain      : 1532 atoms
> > >  6 MainChain+Cb    : 1892 atoms
> > >  7 MainChain+H     : 1896 atoms
> > >  8 SideChain      : 4259 atoms
> > >  9 SideChain-H     : 1562 atoms
> > > 10 Prot-Masses     : 6155 atoms
> > > 11 Non-Protein     : 47849 atoms
> > > 12 SOL         : 47841 atoms
> > > 13 NA+         :   8 atoms
> > > 14 Other        : 47849 atoms
> > > *******
> > > Shoud I edit some other file?
> >
> > use the option which selects atoms based on their
> > numbers (check your pdb file to see the range for
> > each chain).
>
> Or use the output pdb file from pdb2gmx (pdb2gmx -q out.pdb) as  input
> for make_ndx
>