I did use -ter and chose -COO and NH3+. Am i supposed to chose Zwitterion_COO- and Zwitterion_NH3+ ? <br><br><div class="gmail_quote">On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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 class="im"><br>
<br>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
<br>
I have figured out the vacuum slow problem. It turns out I was using PBC in vacuum with PME. It is now fixed.<br>
<br>
The other problem is still there. My protein has 2 chains. one chain is simply a glutamate residue. Its charge (both terminii charged is -1.11 instead of -1). here is the section of the topology with the charges. Why does pdb2gmx assign a charge of -1.11 instead of -1 if there is a free glutamate molecule with NH3+ and COO- at the terminii ? <br>
</blockquote>
<br></div>
You're not choosing the termini correctly. Use -ter with pdb2gmx and select the zwitterion forms of both termini.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
1 opls_287 484 GLU N 1 -0.3 14.0067 ; qtot -0.3<br>
2 opls_290 484 GLU H1 1 0.33 1.008 ; qtot 0.03<br>
3 opls_290 484 GLU H2 1 0.33 1.008 ; qtot 0.36<br>
4 opls_290 484 GLU H3 1 0.33 1.008 ; qtot 0.69<br>
5 opls_283 484 GLU CA 1 0.04 12.011 ; qtot 0.73<br>
6 opls_140 484 GLU HA 1 0.06 1.008 ; qtot 0.79<br>
7 opls_136 484 GLU CB 2 -0.12 12.011 ; qtot 0.67<br>
8 opls_140 484 GLU HB1 2 0.06 1.008 ; qtot 0.73<br>
9 opls_140 484 GLU HB2 2 0.06 1.008 ; qtot 0.79<br>
10 opls_274 484 GLU CG 3 -0.22 12.011 ; qtot 0.57<br>
11 opls_140 484 GLU HG1 3 0.06 1.008 ; qtot 0.63<br>
12 opls_140 484 GLU HG2 3 0.06 1.008 ; qtot 0.69<br>
13 opls_271 484 GLU CD 4 0.7 12.011 ; qtot 1.39<br>
14 opls_272 484 GLU OE1 4 -0.8 15.9994 ; qtot 0.59<br>
15 opls_272 484 GLU OE2 4 -0.8 15.9994 ; qtot -0.21<br>
16 opls_271 484 GLU C 5 0.7 12.011 ; qtot 0.49<br>
17 opls_272 484 GLU O1 5 -0.8 15.9994 ; qtot -0.31<br>
18 opls_272 484 GLU O2 5 -0.8 15.9994 ; qtot -1.11<br>
<br>
<br>
<br></div><div class="im">
On Thu, Jan 20, 2011 at 11:55 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>
<br>
<br>
On 01/20/11, *maria goranovic * <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
<br>
I have a protein whose topology I built using pdb2gmx with the -ss<br>
option and the opls-aa force field. When I run grompp, the total<br>
charge on the protein is reported as 2.9 (not 2.999). Why a<br>
non-zero charge? Does this have something to do with the disulfide<br>
bridge?<br>
</blockquote>
<br>
Something is materially wrong, like mangled termini. Have a look at<br>
the resulting structure.<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Secondly, when I run a simulation of the same protein (7000 atoms)<br>
with certain restraints in vacuum, the simulation runs very slow.<br>
I am wondering why. I am not using particle decomposition. the box<br>
size is 50 x 50 x 50 nm. Using 4.5.3<br>
</blockquote>
<br>
Have a look at the end of the .log file for some performance data.<br>
How are you assessing "very slow"?<br>
<br>
Mark<br>
--<br>
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<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
</div></blockquote>
<br>
-- <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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>