[gmx-users] energy groups

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 3 02:05:21 CET 2009

Liu Shiyong wrote:
> 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
> + editconf -f a6.gro -o a6.gro -d 20.0
> + make_ndx -f a.pdb -o a6.ndx
> + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr

I think you still don't need two invocations of pdb2gmx. Your only 
constraint is that you want chain IDs preserved for your make_ndx 
command. The PDB format carries the system size just like the GRO 
format. Thus

+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr

Simpler still is to define your index groups using information other 
than the chain ID - as I think someone suggested days ago. Ranges of 
atom numbers are also effective.

>         -------------------------------------------------------
>                       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?

Not necessarily - the assignment of energy groups in the .mdp file is 
still a potential source of problems.


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