[gmx-users] problem with make_ndx

Anushree Tripathi anushritripathi at gmail.com
Thu Feb 2 08:06:54 CET 2012 

Yes I want to simulate the protein inside DPPC bilayer but how could I make
the index file. Everytime  it is showing error that no DPPC found in index
file.

On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai <pcl at uab.edu> wrote:

> Are you actually trying to simulate a membrane protein inside a DPPC
> bilayer
> though? If not, what is your reason for having it in your system?
>
> Also the topol.top file does not contain coordinates at all, only the
> forcefield parameterization.
>
> On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote:
> > Please suggest me the exact way to include dppc coordinates in topol.top
> > file.
> >
> > On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> >wrote:
> >
> > >  On 1/02/2012 6:25 PM, Anushree Tripathi wrote:
> > >
> > > But in coordinate file(.pdb file) ,I am not getting the atoms which
> > > belongs to DPPC.
> > >
> > >
> > > You cannot do anything unless you have a coordinate file that includes
> > > DPPC coordinates. I don't know how to express this any more clearly.
> > >
> > >
> > > only I have included the name of dppc.itp file like this:
> > > ;Include DPPC chain topology
> > > #include "dppc.itp"
> > >
> > > That's why I have found the atoms wich belongs to DPPC molecule from
> > > dppc.itp file itself.
> > >
> > >
> > > These numbers are not useful, as I have already explained.
> > >
> > > Mark
> > >
> > >
> > >
> > >
> > > On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> >wrote:
> > >
> > >>  On 1/02/2012 6:04 PM, Anushree Tripathi wrote:
> > >>
> > >> When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is
> > >> showing the following options:
> > >>  0 System              : 18379 atoms
> > >>   1 Protein             : 11739 atoms
> > >>   2 Protein-H           :  9135 atoms
> > >>   3 C-alpha             :  1173 atoms
> > >>   4 Backbone            :  3519 atoms
> > >>   5 MainChain           :  4693 atoms
> > >>   6 MainChain+Cb        :  5773 atoms
> > >>   7 MainChain+H         :  5842 atoms
> > >>   8 SideChain           :  5897 atoms
> > >>   9 SideChain-H         :  4442 atoms
> > >>  10 Prot-Masses         : 11739 atoms
> > >>  11 non-Protein         :  6640 atoms
> > >>  12 Water               :  6636 atoms
> > >>  13 SOL                 :  6636 atoms
> > >>  14 non-Water           : 11743 atoms
> > >>  15 Ion                 :     4 atoms
> > >>  16 CL                  :     4 atoms
> > >>  17 Water_and_ions      :  6640 atoms
> > >>
> > >>
> > >>  So your system has 18K atoms, with 11K protein and the rest solvent
> and
> > >> ions. As Justin suggested, this coordinate file does not have DPPC in
> it.
> > >>
> > >>
> > >>
> > >> for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But
> there
> > >> is no option for DPPC (as given in tutorial we have to merge protein
> with
> > >> DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p
> topol.top -n
> > >> index.ndx -o nvt.tpr),it is showing error:
> > >>
> > >> Group DPPC not found in indexfile.
> > >> Maybe you have non-default goups in your mdp file, while not using the
> > >> '-n' option of grompp.
> > >> In that case use the '-n' option.
> > >>
> > >> To troubleshoot the error,I have kept one more group in index.ndx file
> > >> with number of atoms which I found from dppc.itp file(at the end of
> file)
> > >> like this
> > >>
> > >> [DPPC]
> > >> 1    2    3    4    5    6    7    8    9   10   11   12   13   14
> 15
> > >> 16   17   18   19   20   21   22   23   24   25   26   27   28   29
> 30
> > >> 31   32   33   34   35   36   37   38   39   40   41   42   43   44
> 45
> > >> 46   47   48   49   50
> > >>
> > >>
> > >>  These numbers have to reference the atom numbers in the coordinate
> file,
> > >> not the [moleculetype]. Since you've done the latter, you get the
> problem
> > >> with T-coupling groups. But go back and use a coordinate file that
> actually
> > >> has DPPC in it.
> > >>
> > >> Mark
> > >>
> > >>
> > >>
> > >> Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p
> > >> topol.top -n index.ndx -o nvt.tpr),I am getting the following error:
> > >>
> > >> Atom 1 in multiple T-Coupling groups (1 and 2).
> > >>
> > >> Please suggest me the reason as well as solution for this problem.
> > >>
> > >>
> > >>
> > >>
> > >> --
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> > >
> > >
> > >
> > >
> > >
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> --
> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> pcl at uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                  |
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