[gmx-users] problem with make_ndx

[Anushree Tripathi]

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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