[gmx-users] energy groups

[Justin A. Lemkul]

Liu Shiyong wrote:

>         Here is my command.
> 
>          pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o
>         a6.gro
> 
>          pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
> 
> 
>     Why are you running pdb2gmx twice?  Unless you have multiple
>     proteins, and need multiple topologies, you should not be doing this.
> 
> 
> 
> That's because the *.gro file does not include chain id information.
> 
> If I run  make_ndx -f a6.gro -o a6.ndx
> 
> I will get :
> 
> Found 0 atoms with chain identifiers A AND B
>  >
> Found 0 atoms with chain identifier C
> 

Alright, I was just confused why you're running pdb2gmx twice to get the desired 
output.  If you need a .pdb file, then just choose it as your output format the 
first time you run the command.  I would recommend not dealing with multiple 
iterations of the same command; it can lead to confusion.

>          editconf -f a6.gro -o a6.gro -d 20.0
> 
> 
>     You realize that the units of -d are nm, right?  Do you need such a
>     huge solute-box distance?
> 
> I know the units is nm.

Just checking :)

>  
> 

<snip>

>                -------------------------------------------------------
>                Program grompp, VERSION 4.0.2
>                Source code file: grompp.c, line: 150
>                Fatal error:
>                atoms 1 and 2 in charge group 1 of molecule type
>         'Protein_A' are
>                in different energy groups
>                -------------------------------------------------------

There is still some sort of disconnect between topology numbering (which is 
where charge groups are defined), and the structure you are using.  Can you post 
the first *few* lines of your .pdb file, [ atoms ] section of the .top, and the 
relevant index groups?

-Justin

-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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