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On 5/04/2011 5:39 PM, mohsen ramezanpour wrote:
<blockquote
cite="mid:BANLkTi=XagU63CtoUKCLQ023tNSzrroYUQ@mail.gmail.com"
type="cite">Dear Mark<br>
<br>
Thank you for your important notes,I didn't know them.<br>
<br>
Then,Can it be resulted from your sentences , there is not any
way for doing simulation with only some parts of a protein?<br>
What can I do if I need simulating only ACTIVE SITE of a
protein?Do I have to simulate the whole of protein?<br>
Thanks in advance<br>
</blockquote>
<br>
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...)<br>
<br>
Time spent doing background reading can pay off hundred-fold :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=XagU63CtoUKCLQ023tNSzrroYUQ@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Tue, Apr 5, 2011 at 11:58 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
<div class="im">On 5/04/2011 5:09 PM, mohsen ramezanpour
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
Dear Mark<br>
<br>
Actually I don't know why.<br>
I just did the normal process as other my simulations.<br>
<br>
Let me discribe my work in details:<br>
I had a protein and a drug,I separated all residues around
my drug (2 nm in radius) by PYMOL<br>
</blockquote>
<br>
</div>
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.
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
Then I saved the result as protein-new.pdb<br>
So.I used pdb2gmx to generate .top and .gro file for this
.pdb file<br>
</blockquote>
<br>
</div>
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.
<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
I entered the following commands for pdb2gmx:<br>
pdb2gmx -f protein-new.pdb -o protein-new.gro -p
topology.top -water spc -ignh<br>
and I used Gromos 43a1 force field.<br>
<br>
when I want to do EM there are an additional error that
results in crashing the mdrun:<br>
Warning: 1-4 interaction ... your system is exploding<br>
<br>
it says modifying interaction tables!<br>
<br>
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!<br>
</blockquote>
<br>
</div>
Yep, pdb2gmx has generated backbone peptide bonds that aren't
sensible.
<div>
<div class="h5"><br>
<br>
Mark<br>
-- <br>
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</blockquote>
</div>
<br>
</blockquote>
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