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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