[gmx-users] problem with make_ndx

[Anushree Tripathi]

But in coordinate file(.pdb file) ,I am not getting the atoms which belongs
to DPPC.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.


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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