Now I use genion and it says no ions to add?<div><br></div><div><div>Using a coulomb cut-off of 1 nm</div><div>No ions to add and no potential to calculate.</div><div><br></div><div>command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o solions.gro -p finalnoss.top</div>
<div><br></div><br><div class="gmail_quote">On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I checked topology file but going with grompp makes sense. Thank you.<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Well thats the thing. I have checked my pdb files. All residues have <br>
</blockquote>
<br></div>
There aren't charges in a .pdb file, unless you've somehow added them into one of the fields yourself. The file you need to check is your topology. A running value of the net charges is given in the [atoms] directive. Charges are assigned by pdb2gmx based on what is expected in the .rtp file and what you chose to assign in terms of protonation state.<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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 <br>
</blockquote>
<br></div>
genbox reads coordinate files, so I don't know how any charge it prints is meaningful. It tells me there is a zero charge on a lysozyme system that I know has a +8 charge (regardless of whether or not I pass it a topology as well), so don't believe genbox. Believe grompp. The magnitude is indeed due to small rounding errors. It should be interpreted as -1.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained.<br>
<br>
I am using the charmm implemented version of gromacs.<br>
<br>
Pooja <br></div><div><div></div><div>
On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
On 10/07/2010 1:28 AM, Sai Pooja wrote:<br>
<br>
<br>
Hi,<br>
<br>
When I start from a energy minimized protein in vacuum and<br>
solvate it using genbox, the output message says that the<br>
protein has zero charge. So I skip the genion step. I follow<br>
this with energy minimization of the solvated protein followed<br>
by restraining the protein and then doing a short mdrun (as is<br>
the usual procedure outlined in most tutorials). However, when I<br>
run the grompp command as the first step for the position<br>
restrained md, it runs but prints a note saying that the system<br>
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<br>
it okay to continue with this system?<br>
<br>
<br>
I'd believe grompp before genbox. Surely you know already what is in<br>
your system, and thus its total charge. You should already know the<br>
protonation state of all of your relevant protein residues, because<br>
you made choices for them with pdb2gmx.<br>
<br>
Mark<br>
<br>
<br>
<br>
Pooja<br>
<br>
-- Quaerendo Invenietis-Seek and you shall discover.<br>
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<br>
<br>
-- Quaerendo Invenietis-Seek and you shall discover.<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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