Well thats the thing. I have checked my pdb files. All residues have either 0 or integer net charges. The number 0.9999994 seems like a rounding off error especially since the output of genbox says that the system has zero net charge. Again, I encounter this no-zero net charge when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained.<div>
<br></div><div>I am using the charmm implemented version of gromacs.<br><div><br></div><div>Pooja <br><br><div class="gmail_quote">On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 10/07/2010 1:28 AM, Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi,<br>
<br>
When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.9999.<br>
<br>
NOTE 2 [file finalnoss.top, line 8070]:<br>
System has non-zero total charge: -9.999994e-01<br>
<br>
I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system?<br>
</blockquote>
<br></div>
I'd believe grompp before genbox. Surely you know already what is in your system, and thus its total charge. You should already know the protonation state of all of your relevant protein residues, because you made choices for them with pdb2gmx.<br>
<font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Pooja<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
</blockquote>
<br></div><div><div></div><div class="h5">
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