[gmx-users] index file

[ahmet yıldırım]

Dear users,

Firstly thanks for your replies. I have two ligands as I said before.
I will analyze the system together ligands after the simulation is finished.
For example:
I want to plot potential energy of all system (that is, protein+LİGA+LİGB)
by g_energy.
Then,
Should I create the groups as the following?

*energygrps      = Protein    LİGA_LİGB*
tc-grps         = Protein_LİGA_LİGB    Water_and_ions

OR

*energygrps      = Protein    LİGA    LİGB*
tc-grps         = Protein_LİGA_LİGB    Water_and_ions

Thanks

12 Mayıs 2011 18:29 tarihinde lina <lina.lastname at gmail.com> yazdı:

> 2011/5/12 Justin A. Lemkul <jalemkul at vt.edu>:
> >
> >
> > lina wrote:
> >>
> >> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx
> >>
> >> LiGA & LİGB:
> >
> > This is not correct.  You need to use | rather than &.  Using logical and
> > (&) means the index group will contain atoms that are common to both LIGA
> > and LIGB.  If they are distinct entities, the group will be empty.
>  Logical
> > or (|) says merge the two different groups to create one unified group.
>
> Ooops
>
>
> >
> > -Justin
> >
> >> q
> >>
> >> in grompp add -n your.ndx
> >>
> >>
> >> 2011/5/12 ahmet yıldırım <ahmedo047 at gmail.com>:
> >>>
> >>> Dear users,
> >>>
> >>> I have two ligands. I created a special index group that merges the
> >>> protein,
> >>> LiGA and LİGB.
> >>>
> >>> I have the pr.mdp file as the following:
> >>> ...
> >>> energygrps      = Protein    LİGA_LİGB
> >>> tc-grps         = Protein_LİGA_LİGB    Water_and_ions
> >>> ...
> >>>
> >>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
> >>> Fatal error:
> >>> Group LİGA_LİGB not found in indexfile.
> >>>
> >>> I get the fatal error since I dont have a special index group that
> merges
> >>> LiGA and LİGB. should I create two different index file?
> >>>
> >>> Thanks in advance
> >>> --
> >>> Ahmet YILDIRIM
> >>>
> >>> --
> >>> gmx-users mailing list    gmx-users at gromacs.org
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> >>>
> >>
> >>
> >>
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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> >
>
>
>
> --
> Best Regards,
>
> lina
> --
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>



-- 
Ahmet YILDIRIM
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