[gmx-users] problem with make_ndx

[Peter C. Lai]

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.
> >>
> >>
> >>
> >>
> >> --
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> >
> >
> >
> >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >

> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
==================================================================
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			|
==================================================================