[gmx-users] domain decomposition

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 5 09:57:09 CEST 2011

On 5/04/2011 5:39 PM, mohsen ramezanpour wrote:
> Dear Mark
> Thank you for your important notes,I didn't know them.
> Then,Can it  be resulted from your sentences , there is not any way 
> for doing simulation with only some parts of  a protein?
> What can I do if I need simulating only ACTIVE SITE of a protein?Do I 
> have to simulate the whole of protein?
> Thanks in advance

Generally, yes. For example, it is well known that the electrostatic 
influence of the bulk of the protein affects the function of enzymes. 
Polarization of ligand charge density by the environment can have a 
strong effect on all kinds of chemistry, and is one of the chief 
limitations of trying to use the molecular-mechanics static-point-charge 
model. People spend obscene amounts of resources doing QM+MM MD because 
they need to, not because they have too much computer time! (Even these 
models ignore the polarization of the protein on itself... charges 
parameterized on small-molecule model data need have no relevance near a 
catalytic site...)

Time spent doing background reading can pay off hundred-fold :-)


> On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 5/04/2011 5:09 PM, mohsen ramezanpour wrote:
>         Dear Mark
>         Actually I don't know why.
>         I just did the normal process as other my simulations.
>         Let me discribe my work in details:
>         I had a protein and a drug,I separated all residues around my
>         drug (2 nm in radius) by PYMOL
>     You can't do that and hope for sensible results. The protein won't
>     be happy if you expose its hydrophilic core to either a box of
>     solvent or vacuum or implicit solvent.
>         Then I saved the result as protein-new.pdb
>         So.I used pdb2gmx to generate .top and .gro file for this .pdb
>         file
>     pdb2gmx assumes you're giving it reasonable input - i.e. no
>     missing residues in the protein. However, you've generated several
>     chunks of missing residues above. pdb2gmx assumes there's a
>     backbone peptide bond as normal, and this is too long. One can
>     work around this issue, but still be crippled by the first problem.
>         I entered the following commands for pdb2gmx:
>         pdb2gmx  -f  protein-new.pdb  -o  protein-new.gro   -p  
>         topology.top  -water  spc  -ignh
>         and I used Gromos 43a1 force field.
>         when I want to do EM there are an additional error that
>          results in crashing the mdrun:
>         Warning: 1-4 interaction ...  your system is exploding
>         it says modifying interaction tables!
>         Besides,I checked my pdb file,atoms 922 and 943 and 2 others
>         who have bad interactions,all of them are N atom of residues!
>     Yep, pdb2gmx has generated backbone peptide bonds that aren't
>     sensible.
>     Mark
>     -- 
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