Gee. My mistake then. I did not realize the difference between -COO and Zwitterion_COO-.<br><br>However, when I use the zwitterion termini on both ends of the other chain, the total charge is 4.010, which is also *slightly*´ disturbing. I have seen numbers like 2.999999, which are still better. Is 4.010 acceptable within rounding off errors? <br>
<br>thank you for helping<br><br>-Maria <br><br><div class="gmail_quote">On Thu, Jan 20, 2011 at 2:00 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><br>
<br>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I did use -ter and chose -COO and NH3+. Am i supposed to chose Zwitterion_COO- and Zwitterion_NH3+ ? <br>
</blockquote>
<br></div>
That's what I said, and that's what you have, isn't it? A single amino acid that should have both its termini charged?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div>
On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
maria goranovic wrote:<br>
<br>
Hi<br>
<br>
I have figured out the vacuum slow problem. It turns out I was<br>
using PBC in vacuum with PME. It is now fixed.<br>
<br>
The other problem is still there. My protein has 2 chains. one<br>
chain is simply a glutamate residue. Its charge (both terminii<br>
charged is -1.11 instead of -1). here is the section of the<br>
topology with the charges. Why does pdb2gmx assign a charge of<br>
-1.11 instead of -1 if there is a free glutamate molecule with<br>
NH3+ and COO- at the terminii ?<br>
<br>
<br>
You're not choosing the termini correctly. Use -ter with pdb2gmx<br>
and select the zwitterion forms of both termini.<br>
<br>
-Justin<br>
<br>
<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>
On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham<br>
<<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>><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br>
<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>
<mailto:<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>><br></div></div>
<mailto:<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a><div><div></div><div><br>
<mailto:<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>>>> wrote:<br>
<br>
Hi<br>
<br>
I have a protein whose topology I built using pdb2gmx<br>
with the -ss<br>
option and the opls-aa force field. When I run grompp,<br>
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<br>
disulfide<br>
bridge?<br>
<br>
<br>
Something is materially wrong, like mangled termini. Have a<br>
look at<br>
the resulting structure.<br>
<br>
<br>
Secondly, when I run a simulation of the same protein<br>
(7000 atoms)<br>
with certain restraints in vacuum, the simulation runs<br>
very slow.<br>
I am wondering why. I am not using particle<br>
decomposition. the box<br>
size is 50 x 50 x 50 nm. Using 4.5.3<br>
<br>
<br>
Have a look at the end of the .log file for some performance<br>
data.<br>
How are you assessing "very slow"?<br>
<br>
Mark<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br></div></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><div><br>
<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
<br>
<br>
-- Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><div></div><div><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>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
</div></div></blockquote><div><div></div><div>
<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>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>