maria goranovic wrote:
I did use -ter and chose -COO and NH3+. Am i supposed to chose
Zwitterion_COO- and Zwitterion_NH3+ ?
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?
-Justin
On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
maria goranovic wrote:
Hi
I have figured out the vacuum slow problem. It turns out I was
using PBC in vacuum with PME. It is now fixed.
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 ?
You're not choosing the termini correctly. Use -ter with pdb2gmx
and select the zwitterion forms of both termini.
-Justin
1 opls_287 484 GLU N 1 -0.3
14.0067 ; qtot -0.3
2 opls_290 484 GLU H1 1 0.33
1.008 ; qtot 0.03
3 opls_290 484 GLU H2 1 0.33
1.008 ; qtot 0.36
4 opls_290 484 GLU H3 1 0.33
1.008 ; qtot 0.69
5 opls_283 484 GLU CA 1 0.04
12.011 ; qtot 0.73
6 opls_140 484 GLU HA 1 0.06
1.008 ; qtot 0.79
7 opls_136 484 GLU CB 2 -0.12
12.011 ; qtot 0.67
8 opls_140 484 GLU HB1 2 0.06
1.008 ; qtot 0.73
9 opls_140 484 GLU HB2 2 0.06
1.008 ; qtot 0.79
10 opls_274 484 GLU CG 3 -0.22
12.011 ; qtot 0.57
11 opls_140 484 GLU HG1 3 0.06
1.008 ; qtot 0.63
12 opls_140 484 GLU HG2 3 0.06
1.008 ; qtot 0.69
13 opls_271 484 GLU CD 4 0.7
12.011 ; qtot 1.39
14 opls_272 484 GLU OE1 4 -0.8
15.9994 ; qtot 0.59
15 opls_272 484 GLU OE2 4 -0.8
15.9994 ; qtot -0.21
16 opls_271 484 GLU C 5 0.7
12.011 ; qtot 0.49
17 opls_272 484 GLU O1 5 -0.8
15.9994 ; qtot -0.31
18 opls_272 484 GLU O2 5 -0.8
15.9994 ; qtot -1.11
On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> wrote:
On 01/20/11, *maria goranovic * <mariagorano...@gmail.com
<mailto:mariagorano...@gmail.com>
<mailto:mariagorano...@gmail.com
<mailto:mariagorano...@gmail.com>>> wrote:
Hi
I have a protein whose topology I built using pdb2gmx
with the -ss
option and the opls-aa force field. When I run grompp,
the total
charge on the protein is reported as 2.9 (not 2.999). Why a
non-zero charge? Does this have something to do with the
disulfide
bridge?
Something is materially wrong, like mangled termini. Have a
look at
the resulting structure.
Secondly, when I run a simulation of the same protein
(7000 atoms)
with certain restraints in vacuum, the simulation runs
very slow.
I am wondering why. I am not using particle
decomposition. the box
size is 50 x 50 x 50 nm. Using 4.5.3
Have a look at the end of the .log file for some performance
data.
How are you assessing "very slow"?
Mark
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Maria G.
Technical University of Denmark
Copenhagen
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Maria G.
Technical University of Denmark
Copenhagen
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
