[gmx-users] domain decomposition

[mohsen ramezanpour]

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




On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham <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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