[gmx-users] problem with make_ndx

[Mark Abraham]

On 2/02/2012 5:41 PM, Anushree Tripathi wrote:
> Please suggest me the exact way to include dppc coordinates in 
> topol.top file.

Start here 
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations, as I 
think Justin already suggested. You should definitely learn (about) 
other people's workflows before attempting to adapt them to your needs.

Mark

>
> On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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 <mailto: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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